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comparison tools/blast_rbh/README.rst @ 5:8f4500f6f2aa draft

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Refactored to use more than one Python file (internal change only).
author peterjc
date Tue, 06 Dec 2022 15:53:36 +0000
parents d8d9a9069586
children b2f91cbed8d9
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4:d8d9a9069586 5:8f4500f6f2aa
22 Please cite the following paper: 22 Please cite the following paper:
23 23
24 NCBI BLAST+ integrated into Galaxy. 24 NCBI BLAST+ integrated into Galaxy.
25 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo 25 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
26 *GigaScience* 2015, 4:39 26 *GigaScience* 2015, 4:39
27 DOI: http://dx.doi.org/10.1186/s13742-015-0080-7 27 https://doi.org/10.1186/s13742-015-0080-7
28 28
29 You should also cite the NCBI BLAST+ tools: 29 You should also cite the NCBI BLAST+ tools:
30 30
31 BLAST+: architecture and applications. 31 BLAST+: architecture and applications.
32 C. Camacho et al. *BMC Bioinformatics* 2009, 10:421. 32 C. Camacho et al. *BMC Bioinformatics* 2009, 10:421.
33 DOI: http://dx.doi.org/10.1186/1471-2105-10-421 33 https://doi.org/10.1186/1471-2105-10-421
34 34
35 35
36 Automated Installation 36 Automated Installation
37 ====================== 37 ======================
38 38
41 41
42 42
43 Manual Installation 43 Manual Installation
44 =================== 44 ===================
45 45
46 There are just two files to install: 46 There are just three files to install:
47 47
48 - ``blast_rbh.py`` (the Python script) 48 - ``blast_rbh.py`` (the Python script)
49 - ``best_hits.py`` (helper script, put in same directory)
49 - ``blast_rbh.xml`` (the Galaxy tool definition) 50 - ``blast_rbh.xml`` (the Galaxy tool definition)
50 51
51 The suggested location is in a ``tools/blast_rbh/`` folder. You will then 52 The suggested location is in a ``tools/blast_rbh/`` folder. You will then
52 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool 53 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
53 by adding the line:: 54 by adding the line::
89 - PEP8 style updates to the Python script (internal change only). 90 - PEP8 style updates to the Python script (internal change only).
90 - Fix parameter help text which was not being displayed. 91 - Fix parameter help text which was not being displayed.
91 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. 92 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda.
92 - Update Biopython dependency. 93 - Update Biopython dependency.
93 - Tweak Python script to work under Python 2 or Python 3. 94 - Tweak Python script to work under Python 2 or Python 3.
95 v0.1.12 - Use ``<command detect_errors="aggressive">`` (internal change only).
96 - Single quote command line arguments (internal change only).
97 v0.2.0 - Refactored to use more than one Python file (internal change only).
94 ======= ====================================================================== 98 ======= ======================================================================
95 99
96 100
97 Developers 101 Developers
98 ========== 102 ==========
114 118
115 To just build and check the tar ball, use:: 119 To just build and check the tar ball, use::
116 120
117 $ planemo shed_upload --tar_only tools/blast_rbh/ 121 $ planemo shed_upload --tar_only tools/blast_rbh/
118 ... 122 ...
119 $ tar -tzf shed_upload.tar.gz 123 $ tar -tzf shed_upload.tar.gz
120 test-data/four_human_proteins.fasta 124 test-data/four_human_proteins.fasta
121 test-data/k12_edited_proteins.fasta 125 test-data/k12_edited_proteins.fasta
122 test-data/k12_ten_proteins.fasta 126 test-data/k12_ten_proteins.fasta
123 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular 127 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
124 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular 128 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular