Mercurial > repos > davidvanzessen > igblast_human
changeset 55:99541760fdfe draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 23 Jan 2014 05:35:59 -0500 |
| parents | ddc765e7142c |
| children | 33cba576e8be |
| files | database.zip igblastn.sh igblastn.xml tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 13 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igblastn.sh Thu Jan 23 05:35:59 2014 -0500 @@ -0,0 +1,7 @@ +dir="$(cd "$(dirname "$0")" && pwd)" +echo "dir = $dir" +echo "pwd = $PWD" +mkdir $PWD/igblastdatabase +unzip $dir/database.zip -d $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
--- a/igblastn.xml Tue Dec 03 04:33:59 2013 -0500 +++ b/igblastn.xml Thu Jan 23 05:35:59 2014 -0500 @@ -1,7 +1,7 @@ <tool id="igblastn" name="igBLASTn" version="0.1.0"> <description>Run igBLASTn</description> - <command> - igblastn -germline_db_V \$IGDATA/database/human_gl_V -germline_db_J \$IGDATA/database/human_gl_J -germline_db_D \$IGDATA/database/human_gl_D -domain_system imgt -query $input -auxiliary_data \$IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $output + <command interpreter="bash"> + igblastn.sh $input $output </command> <inputs> <param name="input" type="data" format="fasta" label="Fasta file"/>
--- a/tool_dependencies.xml Tue Dec 03 04:33:59 2013 -0500 +++ b/tool_dependencies.xml Thu Jan 23 05:35:59 2014 -0500 @@ -21,20 +21,10 @@ <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable> </action> - - <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action> - <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action> - - <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data"</action> - - <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/database"</action> - - <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file"</action> - </actions> </install> <readme> - Downloads igBlast with the latest database provided by NCBI, output may change depending on the database available at ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/ + Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool. </readme> </package> </tool_dependency>