Mercurial > repos > peterjc > blast_rbh
changeset 28:a168be0dbd4f draft
v0.1.11 using BLAST+ 2.5.0 and Biopython 1.67
author | peterjc |
---|---|
date | Wed, 19 Apr 2017 07:07:00 -0400 |
parents | f2693e05e16b |
children | 0afb4d0865db |
files | tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/tool_dependencies.xml |
diffstat | 3 files changed, 13 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/blast_rbh/README.rst Mon Apr 03 15:30:37 2017 -0400 +++ b/tools/blast_rbh/README.rst Wed Apr 19 07:07:00 2017 -0400 @@ -88,8 +88,9 @@ v0.1.9 - Updates to the command line API for the Python script. - PEP8 style updates to the Python script (internal change only). - Fix parameter help text which was not being displayed. -v0.1.10 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. -v0.1.11 - Tweak Python script to work under Python 2 or Python 3. +v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. + - Update Biopython dependency. + - Tweak Python script to work under Python 2 or Python 3. ======= ====================================================================== @@ -103,17 +104,17 @@ 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 -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_update -t testtoolshed --check_diff tools/blast_rbh/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_update -t toolshed --check_diff tools/blast_rbh/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_upload --tar_only tools/blast_rbh/ ... $ tar -tzf shed_upload.tar.gz test-data/four_human_proteins.fasta
--- a/tools/blast_rbh/blast_rbh.xml Mon Apr 03 15:30:37 2017 -0400 +++ b/tools/blast_rbh/blast_rbh.xml Wed Apr 19 07:07:00 2017 -0400 @@ -1,8 +1,8 @@ -<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.10"> +<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11"> <description>from two FASTA files</description> <requirements> - <requirement type="package" version="1.64">biopython</requirement> - <requirement type="package" version="2.2.31">blast+</requirement> + <requirement type="package" version="1.67">biopython</requirement> + <requirement type="package" version="2.5.0">blast</requirement> </requirements> <stdio> <!-- Anything other than zero is an error -->
--- a/tools/blast_rbh/tool_dependencies.xml Mon Apr 03 15:30:37 2017 -0400 +++ b/tools/blast_rbh/tool_dependencies.xml Wed Apr 19 07:07:00 2017 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.64"> - <repository changeset_revision="bc1d7fa4ad08" name="package_biopython_1_64" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="blast+" version="2.2.31"> - <repository changeset_revision="803954bd4ff7" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="blast" version="2.5.0"> + <repository changeset_revision="de5976f2c96d" name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>