Mercurial > repos > davidvanzessen > igblast_human
changeset 62:a700a552f031 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 20 Aug 2014 10:04:09 -0400 |
| parents | 39a916965683 |
| children | 7997fea1f16a |
| files | databasenew.zip igblastn.sh igblastn.xml tool_dependencies.xml |
| diffstat | 4 files changed, 1 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/igblastn.sh Thu Jan 23 08:32:42 2014 -0500 +++ b/igblastn.sh Wed Aug 20 10:04:09 2014 -0400 @@ -1,9 +1,7 @@ dir="$(cd "$(dirname "$0")" && pwd)" -echo "dir = $dir" -echo "pwd = $PWD" mkdir $PWD/igblastdatabase unzip $dir/database.zip -d $PWD/igblastdatabase/ export IGDATA=$PWD/igblastdatabase/ -igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $2 +/home/galaxy/galaxy/igblast/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $2
--- a/igblastn.xml Thu Jan 23 08:32:42 2014 -0500 +++ b/igblastn.xml Wed Aug 20 10:04:09 2014 -0400 @@ -10,9 +10,6 @@ <data name="output" format="text" label="${input.name}-igBLASTn Report"/> <!--<data name="log" format="text" label="log"/>--> </outputs> - <requirements> - <requirement type="package" version="1.0.0">igBlastn</requirement> - </requirements> <help> Step 1 of the Immune Repertoire tools, generates a report to be parsed with the "igparse" tool. </help>
--- a/tool_dependencies.xml Thu Jan 23 08:32:42 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - </set_environment> - - <package name="igBlastn" version="1.0.0"> - <install version="1.0"> - <actions> - <action type="shell_command">wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz -P $INSTALL_DIR</action> - <action type="shell_command">tar zxvf $INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux.tar.gz -C $INSTALL_DIR</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool. - </readme> - </package> -</tool_dependency>