Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/README.rst @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
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date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | 70e7dcbf6573 |
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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 2010-2013 by Peter Cock, The James Hutton Institute |
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
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6 See the licence text below. |
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7 |
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8 Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 of BLAST+), |
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9 and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). |
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10 |
70e7dcbf6573
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11 Note that these wrappers (and the associated datatypes) were originally |
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12 distributed as part of the main Galaxy repository, but as of August 2012 |
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13 moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``). |
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14 My thanks to Dannon Baker from the Galaxy development team for his assistance |
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15 with this. |
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16 |
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17 These wrappers are available from the Galaxy Tool Shed at: |
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18 http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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19 |
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20 |
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21 Automated Installation |
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22 ====================== |
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23 |
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24 Galaxy should be able to automatically install the dependencies, i.e. the |
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25 ``blast_datatypes`` repository which defines the BLAST XML file format |
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26 (``blastxml``) and protein and nucleotide BLAST databases (``blastdbp`` and |
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27 ``blastdbn``). |
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28 |
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29 You must tell Galaxy about any system level BLAST databases using configuration |
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30 files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein |
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31 databases like NR), and blastdb_d.loc (protein domain databases like CDD or |
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32 SMART) which are located in the tool-data/ folder. Sample files are included |
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33 which explain the tab-based format to use. |
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34 |
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35 You can download the NCBI provided databases as tar-balls from here: |
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36 |
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37 * ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) |
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38 * ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) |
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39 |
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40 |
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41 Manual Installation |
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42 =================== |
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43 |
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44 For those not using Galaxy's automated installation from the Tool Shed, put |
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45 the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the |
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46 XML files to your ``tool_conf.xml`` as normal (and do the same in |
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47 ``tool_conf.xml.sample`` in order to run the unit tests). For example, use:: |
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48 |
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49 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> |
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50 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> |
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51 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> |
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52 <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> |
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53 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> |
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54 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> |
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55 <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> |
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56 <tool file="ncbi_blast_plus/ncbi_dustmasker_wrapper.xml" /> |
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57 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> |
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58 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> |
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59 <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> |
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60 <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> |
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61 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> |
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62 </section> |
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63 |
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64 You will also need to install ``blast_datatypes`` from the Tool Shed. This |
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65 defines the BLAST XML file format (``blastxml``) and protein and nucleotide |
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66 BLAST databases composite file formats (``blastdbp`` and ``blastdbn``): |
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67 |
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68 * http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes |
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69 |
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70 As described above for an automated installation, you must also tell Galaxy |
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71 about any system level BLAST databases using the ``tool-data/blastdb*.loc`` |
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72 files. |
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73 |
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74 You must install the NCBI BLAST+ standalone tools somewhere on the system |
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75 path. Currently the unit tests are written using "BLAST 2.2.28+". |
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76 |
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77 Run the functional tests (adjusting the section identifier to match your |
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78 ``tool_conf.xml.sample`` file):: |
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79 |
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80 ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools |
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81 |
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82 |
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83 History |
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84 ======= |
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85 |
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86 ======= ====================================================================== |
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87 Version Changes |
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88 ------- ---------------------------------------------------------------------- |
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89 v0.0.11 - Final revision as part of the Galaxy main repository, and the |
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90 first release via the Tool Shed |
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91 v0.0.12 - Implements genetic code option for translation searches. |
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92 - Changes <parallelism> to 1000 sequences at a time (to cope with |
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93 very large sets of queries where BLAST+ can become memory hungry) |
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94 - Include warning that BLAST+ with subject FASTA gives pairwise |
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95 e-values |
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96 v0.0.13 - Use the new error handling options in Galaxy (the previously |
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97 bundled hide_stderr.py script is no longer needed). |
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98 v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases |
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99 in the history (using work from Edward Kirton), requires v0.0.14 |
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100 of the 'blast_datatypes' repository from the Tool Shed. |
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101 v0.0.15 - Stronger warning in help text against searching against subject |
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102 FASTA files (better looking e-values than you might be expecting). |
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103 v0.0.16 - Added repository_dependencies.xml for automates installation of the |
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104 'blast_datatypes' repository from the Tool Shed. |
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105 v0.0.17 - The BLAST+ search tools now default to extended tabular output |
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106 (all too often our users where having to re-run searches just to |
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107 get one of the missing columns like query or subject length) |
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108 v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, |
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109 BLAST+ handling of some mult-file arguments is problematic). |
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110 v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc |
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111 for the domain databases they use (e.g. CDD, PFAM or SMART). |
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112 - Correct case of exception regular expression (for error handling |
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113 fall-back in case the return code is not set properly). |
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114 - Clearer naming of output files. |
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115 v0.0.20 - Added unit tests for BLASTN and TBLASTX. |
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116 - Added percentage identity option to BLASTN. |
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117 - Fallback on ElementTree if cElementTree missing in XML to tabular. |
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118 - Link to Tool Shed added to help text and this documentation. |
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119 - Tweak dependency on blast_datatypes to also work on Test Tool Shed. |
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120 - Dependency on new package_blast_plus_2_2_26 in Tool Shed. |
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121 - Adopted standard MIT License. |
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122 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast |
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123 - Updated citation information (Cock et al. 2013). |
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124 v0.0.21 - Use macros to simplify the XML wrappers. |
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125 - Added wrapper for dustmasker |
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126 - Enabled masking for makeblastdb |
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127 - Requires 'maskinfo-asn1' and 'maskinfo-asn1-binary' datatypes |
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128 defined in updated blast_datatypes on Galaxy ToolShed. |
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129 - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26 |
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130 - Now depends on package_blast_plus_2_2_27 in ToolShed |
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131 v0.0.22 - More use macros to simplify the wrappers |
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132 - Set number of threads via $GALAXY_SLOTS environment variable |
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133 - More descriptive default output names |
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134 - Tests require updated BLAST DB definitions (blast_datatypes v0.0.18) |
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135 - Pre-check for duplicate identifiers in makeblastdb wrapper. |
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136 - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27 |
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137 - Now depends on package_blast_plus_2_2_28 in ToolShed |
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138 - Extended tabular output includes 'salltitles' as column 25. |
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139 ======= ====================================================================== |
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140 |
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141 |
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142 Bug Reports |
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143 =========== |
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144 |
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145 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask |
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146 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev |
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147 |
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148 |
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149 Developers |
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150 ========== |
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151 |
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152 This script and related tools were originally developed on the 'tools' branch |
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153 of the following Mercurial repository: |
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154 https://bitbucket.org/peterjc/galaxy-central/ |
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155 |
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156 As of July 2013, development is continuing on a dedicated GitHub repository: |
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157 https://github.com/peterjc/galaxy_blast |
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158 |
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159 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use |
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160 the following command from the GitHub repository root folder:: |
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161 |
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162 $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh |
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163 |
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164 This simplifies ensuring a consistent set of files is bundled each time, |
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165 including all the relevant test files. |
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166 |
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167 When updating the version of BLAST+, many of the sample data files used for |
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168 the unit tests must be regenerated. This script automates that task:: |
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169 |
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170 $ tools/ncbi_blast_plus/update_test_files.sh |
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171 |
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172 |
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173 Licence (MIT) |
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174 ============= |
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175 |
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176 Permission is hereby granted, free of charge, to any person obtaining a copy |
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177 of this software and associated documentation files (the "Software"), to deal |
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178 in the Software without restriction, including without limitation the rights |
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179 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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180 copies of the Software, and to permit persons to whom the Software is |
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181 furnished to do so, subject to the following conditions: |
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182 |
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183 The above copyright notice and this permission notice shall be included in |
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184 all copies or substantial portions of the Software. |
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185 |
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186 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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187 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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188 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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189 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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190 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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191 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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192 THE SOFTWARE. |