Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/README.rst @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
---|---|
date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 7538e2bfcd41 |
children | 31e517610e1f |
rev | line source |
---|---|
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
1 Galaxy wrappers for NCBI BLAST+ suite |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
2 ===================================== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
3 |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
4 These wrappers are copyright 2010-2017 by Peter Cock (The James Hutton Institute, |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
5 UK) and additional contributors including Edward Kirton, John Chilton, |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
6 Nicola Soranzo, Jim Johnson, and Bjoern Gruening. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
7 |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
8 See the licence text below. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
9 |
21
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
10 Note this does not work with the NCBI 'legacy' BLAST suite written in C |
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
11 (e.g. binary name ``blastall``), but its replacement BLAST, which is |
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
12 written in C++ (e.g. binary name ``blastn``). |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
13 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
14 Note that these wrappers (and the associated datatypes) were originally |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
15 distributed as part of the main Galaxy repository, but as of August 2012 |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
16 moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``). |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
17 My thanks to Dannon Baker from the Galaxy development team for his assistance |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
18 with this. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
19 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
20 These wrappers are available from the Galaxy Tool Shed at: |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
21 http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
22 |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
23 In-development test releases are available from the Test Tool Shed at: |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
24 http://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
25 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
26 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
27 Citation |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
28 ======== |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
29 |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
30 Please cite the following paper: |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
31 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
32 NCBI BLAST+ integrated into Galaxy. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
33 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
34 GigaScience, 2015, 4:39 http://dx.doi.org/10.1186/s13742-015-0080-7 |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
35 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
36 You should also cite the NCBI BLAST+ tools: |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
37 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
38 BLAST+: architecture and applications. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
39 C. Camacho et al. BMC Bioinformatics 2009, 10:421. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
40 DOI: http://dx.doi.org/10.1186/1471-2105-10-421 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
41 |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
42 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
43 Automated Installation |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
44 ====================== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
45 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
46 Galaxy should be able to automatically install the dependencies, i.e. the |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
47 BLAST+ binaries and the ``blast_datatypes`` repository which defines the |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
48 BLAST XML file format (``blastxml``), protein and nucleotide BLAST databases |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
49 (``blastdbp`` and ``blastdbn``), and so on. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
50 |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
51 See the configuration notes below. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
52 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
53 Manual Installation |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
54 =================== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
55 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
56 For those not using Galaxy's automated installation from the Tool Shed, put |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
57 the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
58 XML files to your ``tool_conf.xml`` as normal. For example, use:: |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
59 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
60 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
61 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
62 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
63 <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
64 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
65 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
66 <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
67 <tool file="ncbi_blast_plus/ncbi_dustmasker_wrapper.xml" /> |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
68 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
69 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
70 <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
71 <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
72 <tool file="ncbi_blast_plus/ncbi_makeprofiledb.xml" /> |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
73 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
74 </section> |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
75 |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
76 You will also need to install ``blast_datatypes`` from the Tool Shed. This |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
77 defines the BLAST XML file format (``blastxml``), BLAST databases, etc: |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
78 |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
79 * http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
80 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
81 As described above for an automated installation, you must also tell Galaxy |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
82 about any system level BLAST databases using the ``tool-data/blastdb*.loc`` |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
83 files. Also merge the ``tool-data/tool_data_table_conf.xml.sample`` contents |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
84 into your ``tool_data_table_conf.xml`` file. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
85 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
86 You must install the NCBI BLAST+ standalone tools somewhere on the system |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
87 path. Currently the unit tests are written using BLAST+ 2.2.30. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
88 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
89 Run the functional tests (adjusting the section identifier to match your |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
90 ``tool_conf.xml.sample`` file):: |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
91 |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
92 ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
93 |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
94 Configuration |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
95 ============= |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
96 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
97 You must tell Galaxy about any system level BLAST databases using configuration |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
98 files ``blastdb.loc`` (nucleotide databases like NT) and ``blastdb_p.loc`` |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
99 (protein databases like NR), and ``blastdb_d.loc`` (protein domain databases |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
100 like CDD or SMART) which are located in the ``tool-data/`` folder. Sample |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
101 files are included which explain the tab-based format to use. |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
102 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
103 You can download the NCBI provided databases as tar-balls from here: |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
104 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
105 * ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
106 * ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
107 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
108 If using the optional taxonomy columns, you will also need to download the |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
109 NCBI taxonomy files (``taxdb.btd`` and ``taxdb.bti`` from ``taxdb.tar.gz`` on |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
110 the BLAST database FTP site). Currently explicit version tracking of the |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
111 taxonomy is not supported, and in order to use this you must set the |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
112 ``$BLASTDB`` environment variable to include the path where you unzipped the |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
113 taxonomy files. If this is not done, the taxonomy columns like species name |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
114 will appear as ``N/A`` in the tabular output. |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
115 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
116 The BLAST+ binaries support multi-threaded operation, which is handled via the |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
117 ``$GALAXY_SLOTS`` environment variable. This should be set automatically by |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
118 Galaxy via your job runner settings, which allows you to (for example) allocate |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
119 four cores to each BLAST job. |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
120 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
121 In addition, the BLAST+ wrappers also support high level parallelism by task |
20
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
122 splitting if ``use_tasked_jobs = True`` is enabled in the ``config/galaxy.ini`` |
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
123 configuration file (previously ``universe_wsgi.ini`` on older versions of |
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
124 Galaxy). Essentially, the FASTA input query files are broken up into |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
125 batches of 1000 sequences, a separate BLAST child job is run for each chunk, |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
126 and then the BLAST output files are merged (in order). This is transparent |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
127 for the end user. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
128 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
129 History |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
130 ======= |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
131 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
132 ======= ====================================================================== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
133 Version Changes |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
134 ------- ---------------------------------------------------------------------- |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
135 v0.0.11 - Final revision as part of the Galaxy main repository, and the |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
136 first release via the Tool Shed |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
137 v0.0.12 - Implements genetic code option for translation searches. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
138 - Changes ``<parallelism>`` to 1000 sequences at a time (to cope with |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
139 very large sets of queries where BLAST+ can become memory hungry) |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
140 - Include warning that BLAST+ with subject FASTA gives pairwise |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
141 e-values |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
142 v0.0.13 - Use the new error handling options in Galaxy (the previously |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
143 bundled ``hide_stderr.py`` script is no longer needed). |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
144 v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
145 in the history (using work from Edward Kirton), requires v0.0.14 |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
146 of the ``blast_datatypes`` repository from the Tool Shed. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
147 v0.0.15 - Stronger warning in help text against searching against subject |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
148 FASTA files (better looking e-values than you might be expecting). |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
149 v0.0.16 - Added repository_dependencies.xml for automates installation of the |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
150 ``blast_datatypes`` repository from the Tool Shed. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
151 v0.0.17 - The BLAST+ search tools now default to extended tabular output |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
152 (all too often our users where having to re-run searches just to |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
153 get one of the missing columns like query or subject length) |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
154 v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
155 BLAST+ handling of some multi-file arguments is problematic). |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
156 v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc`` |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
157 for the domain databases they use (e.g. CDD, PFAM or SMART). |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
158 - Correct case of exception regular expression (for error handling |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
159 fall-back in case the return code is not set properly). |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
160 - Clearer naming of output files. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
161 v0.0.20 - Added unit tests for BLASTN and TBLASTX. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
162 - Added percentage identity option to BLASTN. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
163 - Fallback on ElementTree if cElementTree missing in XML to tabular. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
164 - Link to Tool Shed added to help text and this documentation. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
165 - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
166 - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed. |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
167 - Adopted standard MIT License. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
168 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
169 - Updated citation information (Cock et al. 2013). |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
170 v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
171 - Added wrapper for dustmasker. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
172 - Enabled masking for makeblastdb (Nicola Soranzo). |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
173 - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes, |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
174 defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed. |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
175 - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
176 - Now depends on ``package_blast_plus_2_2_27`` in ToolShed. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
177 v0.0.22 - More use of macros to simplify the wrappers. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
178 - Set number of threads via ``$GALAXY_SLOTS`` environment variable. |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
179 - More descriptive default output names. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
180 - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18). |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
181 - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
182 - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
183 - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
184 - Extended tabular output includes 'salltitles' as column 25. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
185 v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
186 - Tabular output now includes option to pick specific columns |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
187 (based on contribution from Jim Johnson), including previously |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
188 unavailable taxonomy columns. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
189 - BLAST XML to tabular tool supports multiple input files |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
190 (based on contribution from Jim Johnson). |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
191 - More detailed descriptions for BLASTN and BLASTP task option. |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
192 - Wrappers for segmasker, dustmasker and convert2blastmask |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
193 (contribution from Bjoern Gruening). |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
194 - Supports using maskinfo with ``makeblastdb`` wrapper. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
195 - Supports setting a taxonomy ID in ``makeblastdb`` wrapper. |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
196 - Subtle changes like new conditional settings will require some old |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
197 workflows be updated to cope. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
198 v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
199 - Wrapper for makeprofiledb added to create protein domain databases |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
200 (based on contribution from Bjoern Gruening). |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
201 - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
202 domain database from the user's history. |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
203 - Tool definitions now embed citation information (by John Chilton). |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
204 - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
205 v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
206 - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
207 - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
208 - New minimum query HSP coverage option, ``-qcov_hsp_perc``. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
209 - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
210 is set during database construction and should not have been offered |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
211 as a command line option in releases prior to BLAST+ 2.2.30. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
212 - BLAST database ``blastdb*.loc`` files now accessed via the XML |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
213 table definitions in Galaxy's ``tool_data_table_conf.xml`` file, |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
214 setup via ``tool-data/tool_data_table_conf.xml.sample`` |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
215 - Replace ``.extra_files_path`` with ``.files_path`` (internal change, |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
216 thanks to Bjoern Gruening and John Chilton). |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
217 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
218 v0.1.03 - Reorder XML elements (internal change only). |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
219 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). |
16
b5f1f599d1fb
Uploaded v0.1.04, fix regression with BLAST database from history
peterjc
parents:
15
diff
changeset
|
220 v0.1.04 - Fixed regression using BLAST databases from the history. Currently |
b5f1f599d1fb
Uploaded v0.1.04, fix regression with BLAST database from history
peterjc
parents:
15
diff
changeset
|
221 Galaxy inputs must still use ``.extra_files_path`` rather than the |
b5f1f599d1fb
Uploaded v0.1.04, fix regression with BLAST database from history
peterjc
parents:
15
diff
changeset
|
222 more consise ``.extra_files`` available for output files (Issue #69) |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
223 v0.1.05 - Define ``parallelism`` tag via a macro (internal change only). |
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
224 - Define wrapper versions via a macro (internal change only). |
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
225 - Update citation information now GigaScience paper is out. |
18 | 226 v0.1.06 - Now depends on ``package_blast_plus_2_2_31`` in ToolShed. |
227 - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30. | |
19
7f3c448e119b
v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests
peterjc
parents:
18
diff
changeset
|
228 v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported |
7f3c448e119b
v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests
peterjc
parents:
18
diff
changeset
|
229 on the Tool Shed test framework, but that is not currently in use). |
7f3c448e119b
v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests
peterjc
parents:
18
diff
changeset
|
230 - Fixed macro problem with version field in blastxml_to_tabular.xml |
7f3c448e119b
v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests
peterjc
parents:
18
diff
changeset
|
231 (contribution from Bjoern Gruening and Daniel Blankenberg). |
20
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
232 v0.1.08 - Allow searching against multiple locally installed databases |
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
233 (contribution from Gildas Le Corguillé and Emma Prudent). |
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
234 - Minor XML and Python style changes (internal change only). |
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
235 - Set ``allow_duplicate_entries="False"`` in sample configuration file |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
236 ``tool_data_table_conf.xml``. |
20
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
237 - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). |
21
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
238 v0.2.00 - Updated for NCBI BLAST+ 2.5.0, where GI numbers are less visible, |
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
239 tabular output changes with `-parse_deflines`, and percentage |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
240 identifies are now given to 3dp rather than 2dp. |
21
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
241 - Depends on ``package_blast_plus_2_5_0`` in ToolShed, or BioConda. |
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
242 - ``blastxml_to_tabular`` now also gives percentage idenity to 3dp. |
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
243 - Removed never-used binary and Python module dependency declarations |
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
244 (internal change only). |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
245 v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only). |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
246 - Single quote command line arguments (internal change only). |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
247 - Show BLAST command line argument corresponding to each tool |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
248 parameter (contribution from Nicola Soranzo). |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
249 - Add ``-max_hsps`` option (contribution from Nicola Soranzo). |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
250 - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
251 ======= ====================================================================== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
252 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
253 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
254 Bug Reports |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
255 =========== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
256 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
257 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
258 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
259 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
260 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
261 Developers |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
262 ========== |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
263 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
264 This script and related tools were originally developed on the 'tools' branch |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
265 of the following Mercurial repository: |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
266 https://bitbucket.org/peterjc/galaxy-central/ |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
267 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
268 As of July 2013, development is continuing on a dedicated GitHub repository: |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
269 https://github.com/peterjc/galaxy_blast |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
270 |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
271 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
272 Planemo commands (which requires you have set your Tool Shed access details in |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
273 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
274 |
21
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
275 $ planemo shed_update -t testtoolshed --check_diff tools/ncbi_blast_plus/ |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
276 ... |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
277 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
278 or:: |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
279 |
21
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
280 $ planemo shed_update -t toolshed --check_diff tools/ncbi_blast_plus/ |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
281 ... |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
282 |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
283 To just build and check the tar ball, use:: |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
284 |
21
7538e2bfcd41
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
peterjc
parents:
20
diff
changeset
|
285 $ planemo shed_upload --tar_only tools/ncbi_blast_plus/ |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
286 ... |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
287 $ tar -tzf shed_upload.tar.gz |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
288 test-data/blastdb.loc |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
289 ... |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
290 tools/ncbi_blast_plus/tool_dependencies.xml |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
291 $ tar -tzf shed_upload.tar.gz | wc -l |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
292 117 |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
293 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
294 This simplifies ensuring a consistent set of files is bundled each time, |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
295 including all the relevant test files. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
296 |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
297 When updating the version of BLAST+, many of the sample data files used for |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
298 the unit tests must be regenerated. This script automates that task:: |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
299 |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
300 $ tools/ncbi_blast_plus/update_test_files.sh |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
10
diff
changeset
|
301 |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
302 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
303 Licence (MIT) |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
304 ============= |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
305 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
306 Permission is hereby granted, free of charge, to any person obtaining a copy |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
307 of this software and associated documentation files (the "Software"), to deal |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
308 in the Software without restriction, including without limitation the rights |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
309 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
310 copies of the Software, and to permit persons to whom the Software is |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
311 furnished to do so, subject to the following conditions: |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
312 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
313 The above copyright notice and this permission notice shall be included in |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
314 all copies or substantial portions of the Software. |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
315 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
316 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
317 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
318 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
319 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
320 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
321 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
parents:
diff
changeset
|
322 THE SOFTWARE. |