Mercurial > repos > peterjc > blast_rbh
changeset 3:9ba8ebb636f4 draft
v0.1.8 - Using BLAST+ 2.2.31
| author | peterjc |
|---|---|
| date | Mon, 07 Sep 2015 04:40:51 -0400 |
| parents | 14b2e159b310 |
| children | d8d9a9069586 |
| files | test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/tool_dependencies.xml |
| diffstat | 9 files changed, 23 insertions(+), 22 deletions(-) [+] |
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--- a/test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular Fri Sep 04 07:06:18 2015 -0400 +++ b/test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular Mon Sep 07 04:40:51 2015 -0400 @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -ENA|BC112106|BC112106.1 gi|57163782|ref|NM_001009242.1| 1213 1047 86 100 1047 92.07 1514 +ENA|BC112106|BC112106.1 gi|57163782|ref|NM_001009242.1| 1213 1047 86 100 1047 92.07 1514
--- a/test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular Fri Sep 04 07:06:18 2015 -0400 +++ b/test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular Mon Sep 07 04:40:51 2015 -0400 @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 348 348 100 100 348 96.55 701 +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 348 348 100 100 348 96.55 701
--- a/test-data/rbh_blastp_k12.tabular Fri Sep 04 07:06:18 2015 -0400 +++ b/test-data/rbh_blastp_k12.tabular Mon Sep 07 04:40:51 2015 -0400 @@ -1,10 +1,10 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore gi|16127995|ref|NP_414542.1| gi|16127995|ref|NP_414542.1| 21 21 100 100 21 100.00 38.1 -gi|16127996|ref|NP_414543.1| gi|16127996|ref|NP_414543.1| 820 820 100 100 820 100.00 1687 -gi|16127997|ref|NP_414544.1| gi|16127997|ref|NP_414544.1| 310 310 100 100 310 100.00 642 -gi|16127998|ref|NP_414545.1| gi|16127998|ref|NP_414545.1| 428 428 100 100 428 100.00 882 -gi|16128000|ref|NP_414547.1| gi|16128000|ref|NP_414547.1| 258 258 100 100 258 100.00 531 -gi|16128001|ref|NP_414548.1| gi|16128001|ref|NP_414548.1| 476 476 100 100 476 100.00 959 -gi|16128002|ref|NP_414549.1| gi|16128002|ref|NP_414549.1| 317 317 100 100 317 100.00 648 -gi|16128003|ref|NP_414550.1| gi|16128003|ref|NP_414550.1| 195 195 100 100 195 100.00 397 -gi|16128004|ref|NP_414551.1| gi|16128004|ref|NP_414551.1| 188 188 100 100 188 100.00 365 +gi|16127996|ref|NP_414543.1| gi|16127996|ref|NP_414543.1| 820 820 100 100 820 100.00 1687 +gi|16127997|ref|NP_414544.1| gi|16127997|ref|NP_414544.1| 310 310 100 100 310 100.00 642 +gi|16127998|ref|NP_414545.1| gi|16127998|ref|NP_414545.1| 428 428 100 100 428 100.00 882 +gi|16128000|ref|NP_414547.1| gi|16128000|ref|NP_414547.1| 258 258 100 100 258 100.00 531 +gi|16128001|ref|NP_414548.1| gi|16128001|ref|NP_414548.1| 476 476 100 100 476 100.00 959 +gi|16128002|ref|NP_414549.1| gi|16128002|ref|NP_414549.1| 317 317 100 100 317 100.00 648 +gi|16128003|ref|NP_414550.1| gi|16128003|ref|NP_414550.1| 195 195 100 100 195 100.00 397 +gi|16128004|ref|NP_414551.1| gi|16128004|ref|NP_414551.1| 188 188 100 100 188 100.00 365
--- a/test-data/rbh_blastp_k12_self.tabular Fri Sep 04 07:06:18 2015 -0400 +++ b/test-data/rbh_blastp_k12_self.tabular Mon Sep 07 04:40:51 2015 -0400 @@ -1,5 +1,5 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|16127997|ref|NP_414544.1| NP_414544_near_copy 310 309 99 100 309 99.68 638 -NP_414544_near_copy gi|16127997|ref|NP_414544.1| 309 310 100 99 309 99.68 638 -NP_414546_near_copy_1 NP_414546_near_copy_2 99 100 99 98 98 100.00 197 -NP_414546_near_copy_2 NP_414546_near_copy_1 100 99 98 99 98 100.00 197 +gi|16127997|ref|NP_414544.1| NP_414544_near_copy 310 309 99 100 309 99.68 638 +NP_414544_near_copy gi|16127997|ref|NP_414544.1| 309 310 100 99 309 99.68 638 +NP_414546_near_copy_1 NP_414546_near_copy_2 99 100 99 98 98 100.00 197 +NP_414546_near_copy_2 NP_414546_near_copy_1 100 99 98 99 98 100.00 197
--- a/test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular Fri Sep 04 07:06:18 2015 -0400 +++ b/test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular Mon Sep 07 04:40:51 2015 -0400 @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 100 86 1047 92.07 1474 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 100 86 1047 92.07 1474
--- a/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular Fri Sep 04 07:06:18 2015 -0400 +++ b/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular Mon Sep 07 04:40:51 2015 -0400 @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 22 19 230 97.39 559 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 22 19 230 97.39 559
--- a/tools/blast_rbh/README.rst Fri Sep 04 07:06:18 2015 -0400 +++ b/tools/blast_rbh/README.rst Mon Sep 07 04:40:51 2015 -0400 @@ -84,6 +84,7 @@ v0.1.7 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Updated citation information with GigaScience paper. +v0.1.8 - Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install. ======= ====================================================================== @@ -97,12 +98,12 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ ... or:: - $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ ... To just build and check the tar ball, use::
--- a/tools/blast_rbh/blast_rbh.xml Fri Sep 04 07:06:18 2015 -0400 +++ b/tools/blast_rbh/blast_rbh.xml Mon Sep 07 04:40:51 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.7"> +<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.8"> <description>from two FASTA files</description> <requirements> <requirement type="package" version="1.64">biopython</requirement> @@ -6,7 +6,7 @@ <requirement type="binary">makeblastdb</requirement> <requirement type="binary">blastp</requirement> <requirement type="binary">blastn</requirement> - <requirement type="package" version="2.2.30">blast+</requirement> + <requirement type="package" version="2.2.31">blast+</requirement> </requirements> <stdio> <!-- Anything other than zero is an error -->
--- a/tools/blast_rbh/tool_dependencies.xml Fri Sep 04 07:06:18 2015 -0400 +++ b/tools/blast_rbh/tool_dependencies.xml Mon Sep 07 04:40:51 2015 -0400 @@ -3,7 +3,7 @@ <package name="biopython" version="1.64"> <repository changeset_revision="5477a05cc158" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="blast+" version="2.2.30"> - <repository changeset_revision="0fe5d5c28ea2" name="package_blast_plus_2_2_30" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="blast+" version="2.2.31"> + <repository changeset_revision="e36f75574aec" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>