Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/README.rst @ 16:b5f1f599d1fb draft
Uploaded v0.1.04, fix regression with BLAST database from history
author | peterjc |
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date | Wed, 22 Jul 2015 05:01:11 -0400 |
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1 Galaxy wrappers for NCBI BLAST+ suite |
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2 ===================================== |
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3 |
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4 These wrappers are copyright 2010-2014 by Peter Cock (The James Hutton Institute, |
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5 UK) and additional contributors including Edward Kirton, John Chilton, |
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6 Nicola Soranzo, Jim Johnson, and Bjoern Gruening. |
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7 |
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8 See the licence text below. |
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9 |
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10 Currently tested with NCBI BLAST 2.2.30+ (i.e. version 2.2.30 of BLAST+), |
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11 and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). |
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12 |
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13 Note that these wrappers (and the associated datatypes) were originally |
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14 distributed as part of the main Galaxy repository, but as of August 2012 |
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15 moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``). |
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16 My thanks to Dannon Baker from the Galaxy development team for his assistance |
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17 with this. |
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18 |
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19 These wrappers are available from the Galaxy Tool Shed at: |
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20 http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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21 |
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22 In-development test releases are available from the Test Tool Shed at: |
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23 http://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ |
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24 |
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25 |
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26 Citation |
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27 ======== |
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28 |
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29 Please cite the following paper (currently available as a preprint): |
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30 |
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31 NCBI BLAST+ integrated into Galaxy. |
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32 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo |
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33 bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint) |
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34 |
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35 You should also cite the NCBI BLAST+ tools: |
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36 |
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37 BLAST+: architecture and applications. |
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38 C. Camacho et al. BMC Bioinformatics 2009, 10:421. |
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39 DOI: http://dx.doi.org/10.1186/1471-2105-10-421 |
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40 |
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41 |
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42 Automated Installation |
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43 ====================== |
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44 |
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45 Galaxy should be able to automatically install the dependencies, i.e. the |
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46 BLAST+ binaries and the ``blast_datatypes`` repository which defines the |
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47 BLAST XML file format (``blastxml``), protein and nucleotide BLAST databases |
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48 (``blastdbp`` and ``blastdbn``), and so on. |
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49 |
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50 See the configuration notes below. |
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51 |
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52 Manual Installation |
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53 =================== |
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54 |
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55 For those not using Galaxy's automated installation from the Tool Shed, put |
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56 the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the |
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57 XML files to your ``tool_conf.xml`` as normal. For example, use:: |
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58 |
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59 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> |
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60 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> |
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61 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> |
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62 <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> |
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63 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> |
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64 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> |
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65 <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> |
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66 <tool file="ncbi_blast_plus/ncbi_dustmasker_wrapper.xml" /> |
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67 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> |
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68 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> |
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69 <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> |
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70 <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> |
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71 <tool file="ncbi_blast_plus/ncbi_makeprofiledb.xml" /> |
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72 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> |
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73 </section> |
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74 |
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75 You will also need to install ``blast_datatypes`` from the Tool Shed. This |
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76 defines the BLAST XML file format (``blastxml``), BLAST databases, etc: |
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77 |
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78 * http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes |
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79 |
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80 As described above for an automated installation, you must also tell Galaxy |
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81 about any system level BLAST databases using the ``tool-data/blastdb*.loc`` |
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82 files. Also merge the ``tool-data/tool_data_table_conf.xml.sample`` contents |
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83 into your ``tool_data_table_conf.xml`` file. |
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84 |
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85 You must install the NCBI BLAST+ standalone tools somewhere on the system |
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86 path. Currently the unit tests are written using BLAST+ 2.2.30. |
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87 |
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88 Run the functional tests (adjusting the section identifier to match your |
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89 ``tool_conf.xml.sample`` file):: |
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90 |
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91 ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools |
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92 |
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93 Configuration |
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94 ============= |
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95 |
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96 You must tell Galaxy about any system level BLAST databases using configuration |
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97 files ``blastdb.loc`` (nucleotide databases like NT) and ``blastdb_p.loc`` |
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98 (protein databases like NR), and ``blastdb_d.loc`` (protein domain databases |
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99 like CDD or SMART) which are located in the ``tool-data/`` folder. Sample |
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100 files are included which explain the tab-based format to use. |
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101 |
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102 You can download the NCBI provided databases as tar-balls from here: |
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103 |
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104 * ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) |
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105 * ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) |
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106 |
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107 If using the optional taxonomy columns, you will also need to download the |
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108 NCBI taxonomy files (``taxdb.btd`` and ``taxdb.bti`` from ``taxdb.tar.gz`` on |
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109 the BLAST database FTP site). Currently explicit version tracking of the |
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110 taxonomy is not supported, and in order to use this you must set the |
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111 ``$BLASTDB`` environment variable to include the path where you unzipped the |
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112 taxonomy files. If this is not done, the taxonomy columns like species name |
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113 will appear as ``N/A`` in the tabular output. |
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114 |
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115 The BLAST+ binaries support multi-threaded operation, which is handled via the |
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116 ``$GALAXY_SLOTS`` environment variable. This should be set automatically by |
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117 Galaxy via your job runner settings, which allows you to (for example) allocate |
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118 four cores to each BLAST job. |
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119 |
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120 In addition, the BLAST+ wrappers also support high level parallelism by task |
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121 splitting if ``use_tasked_jobs = True`` is enabled in your ``universe_wsgi.ini`` |
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122 configuration file. Essentially, the FASTA input query files are broken up into |
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123 batches of 1000 sequences, a separate BLAST child job is run for each chunk, |
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124 and then the BLAST output files are merged (in order). This is transparent |
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125 for the end user. |
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126 |
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127 History |
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128 ======= |
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129 |
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130 ======= ====================================================================== |
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131 Version Changes |
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132 ------- ---------------------------------------------------------------------- |
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133 v0.0.11 - Final revision as part of the Galaxy main repository, and the |
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134 first release via the Tool Shed |
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135 v0.0.12 - Implements genetic code option for translation searches. |
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136 - Changes ``<parallelism>`` to 1000 sequences at a time (to cope with |
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137 very large sets of queries where BLAST+ can become memory hungry) |
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138 - Include warning that BLAST+ with subject FASTA gives pairwise |
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139 e-values |
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140 v0.0.13 - Use the new error handling options in Galaxy (the previously |
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141 bundled ``hide_stderr.py`` script is no longer needed). |
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142 v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases |
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143 in the history (using work from Edward Kirton), requires v0.0.14 |
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144 of the ``blast_datatypes`` repository from the Tool Shed. |
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145 v0.0.15 - Stronger warning in help text against searching against subject |
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146 FASTA files (better looking e-values than you might be expecting). |
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147 v0.0.16 - Added repository_dependencies.xml for automates installation of the |
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148 ``blast_datatypes`` repository from the Tool Shed. |
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149 v0.0.17 - The BLAST+ search tools now default to extended tabular output |
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150 (all too often our users where having to re-run searches just to |
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151 get one of the missing columns like query or subject length) |
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152 v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, |
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153 BLAST+ handling of some multi-file arguments is problematic). |
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154 v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc`` |
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155 for the domain databases they use (e.g. CDD, PFAM or SMART). |
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156 - Correct case of exception regular expression (for error handling |
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157 fall-back in case the return code is not set properly). |
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158 - Clearer naming of output files. |
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159 v0.0.20 - Added unit tests for BLASTN and TBLASTX. |
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160 - Added percentage identity option to BLASTN. |
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161 - Fallback on ElementTree if cElementTree missing in XML to tabular. |
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162 - Link to Tool Shed added to help text and this documentation. |
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163 - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed. |
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164 - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed. |
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165 - Adopted standard MIT License. |
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166 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast |
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167 - Updated citation information (Cock et al. 2013). |
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168 v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). |
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169 - Added wrapper for dustmasker. |
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170 - Enabled masking for makeblastdb (Nicola Soranzo). |
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171 - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes, |
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172 defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed. |
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173 - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26. |
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174 - Now depends on ``package_blast_plus_2_2_27`` in ToolShed. |
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175 v0.0.22 - More use of macros to simplify the wrappers. |
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176 - Set number of threads via ``$GALAXY_SLOTS`` environment variable. |
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177 - More descriptive default output names. |
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178 - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18). |
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179 - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. |
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180 - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. |
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181 - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. |
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182 - Extended tabular output includes 'salltitles' as column 25. |
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183 v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed. |
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184 - Tabular output now includes option to pick specific columns |
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185 (based on contribution from Jim Johnson), including previously |
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186 unavailable taxonomy columns. |
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187 - BLAST XML to tabular tool supports multiple input files |
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188 (based on contribution from Jim Johnson). |
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189 - More detailed descriptions for BLASTN and BLASTP task option. |
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190 - Wrappers for segmasker, dustmasker and convert2blastmask |
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191 (contribution from Bjoern Gruening). |
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192 - Supports using maskinfo with ``makeblastdb`` wrapper. |
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193 - Supports setting a taxonomy ID in ``makeblastdb`` wrapper. |
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194 - Subtle changes like new conditional settings will require some old |
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195 workflows be updated to cope. |
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196 v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). |
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197 - Wrapper for makeprofiledb added to create protein domain databases |
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198 (based on contribution from Bjoern Gruening). |
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199 - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein |
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200 domain database from the user's history. |
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201 - Tool definitions now embed citation information (by John Chilton). |
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202 - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). |
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203 v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. |
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204 - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. |
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205 - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. |
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206 - New minimum query HSP coverage option, ``-qcov_hsp_perc``. |
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207 - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this |
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208 is set during database construction and should not have been offered |
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209 as a command line option in releases prior to BLAST+ 2.2.30. |
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210 - BLAST database ``blastdb*.loc`` files now accessed via the XML |
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211 table definitions in Galaxy's ``tool_data_table_conf.xml`` file, |
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212 setup via ``tool-data/tool_data_table_conf.xml.sample`` |
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213 - Replace ``.extra_files_path`` with ``.files_path`` (internal change, |
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214 thanks to Bjoern Gruening and John Chilton). |
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215 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. |
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216 v0.1.03 - Reorder XML elements (internal change only). |
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217 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). |
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218 v0.1.04 - Fixed regression using BLAST databases from the history. Currently |
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219 Galaxy inputs must still use ``.extra_files_path`` rather than the |
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220 more consise ``.extra_files`` available for output files (Issue #69) |
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221 ======= ====================================================================== |
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222 |
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223 |
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224 Bug Reports |
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225 =========== |
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226 |
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227 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask |
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228 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev |
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229 |
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230 |
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231 Developers |
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232 ========== |
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233 |
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234 This script and related tools were originally developed on the 'tools' branch |
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235 of the following Mercurial repository: |
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236 https://bitbucket.org/peterjc/galaxy-central/ |
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237 |
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238 As of July 2013, development is continuing on a dedicated GitHub repository: |
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239 https://github.com/peterjc/galaxy_blast |
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240 |
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241 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
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242 Planemo commands (which requires you have set your Tool Shed access details in |
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243 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
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244 |
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245 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ |
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246 ... |
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247 |
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248 or:: |
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249 |
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250 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ |
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251 ... |
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252 |
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253 To just build and check the tar ball, use:: |
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254 |
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255 $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ |
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256 ... |
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257 $ tar -tzf shed_upload.tar.gz |
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258 test-data/blastdb.loc |
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259 ... |
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260 tools/ncbi_blast_plus/tool_dependencies.xml |
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261 $ tar -tzf shed_upload.tar.gz | wc -l |
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262 117 |
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263 |
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264 This simplifies ensuring a consistent set of files is bundled each time, |
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265 including all the relevant test files. |
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266 |
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267 When updating the version of BLAST+, many of the sample data files used for |
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268 the unit tests must be regenerated. This script automates that task:: |
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269 |
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270 $ tools/ncbi_blast_plus/update_test_files.sh |
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271 |
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272 |
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273 Licence (MIT) |
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274 ============= |
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275 |
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276 Permission is hereby granted, free of charge, to any person obtaining a copy |
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277 of this software and associated documentation files (the "Software"), to deal |
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278 in the Software without restriction, including without limitation the rights |
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279 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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280 copies of the Software, and to permit persons to whom the Software is |
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281 furnished to do so, subject to the following conditions: |
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282 |
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283 The above copyright notice and this permission notice shall be included in |
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284 all copies or substantial portions of the Software. |
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285 |
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286 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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287 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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288 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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289 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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290 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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291 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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292 THE SOFTWARE. |