Mercurial > repos > davidvanzessen > igblast_human
changeset 37:215aa111db64 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 24 Sep 2013 10:42:31 -0400 |
| parents | 1d15cd0bd913 |
| children | cc443e49b89e |
| files | igblastn.xml igblastn.xml~ tool_dependencies.xml |
| diffstat | 3 files changed, 27 insertions(+), 159 deletions(-) [+] |
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--- a/igblastn.xml Tue Sep 24 10:15:19 2013 -0400 +++ b/igblastn.xml Tue Sep 24 10:42:31 2013 -0400 @@ -1,7 +1,7 @@ <tool id="igblastn" name="igBLASTn" version="0.1.0"> <description>Run igBLASTn</description> <command> - igblastn -germline_db_V /usr/local/ncbi-igblast-1.0.0/database/human_gl_V -germline_db_J /usr/local/ncbi-igblast-1.0.0/database/human_gl_J -germline_db_D /usr/local/ncbi-igblast-1.0.0/database/human_gl_D -domain_system imgt -query $input -auxiliary_data /usr/local/ncbi-igblast-1.0.0/optional_file/human_gl.aux -show_translation -outfmt 3 > $output + 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> <inputs> <param name="input" type="data" format="fasta" label="Fasta file"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igblastn.xml~ Tue Sep 24 10:42:31 2013 -0400 @@ -0,0 +1,19 @@ +<tool id="igblastn" name="igBLASTn" version="0.1.0"> + <description>Run igBLASTn</description> + <command> + igblastn -germline_db_V /usr/local/ncbi-igblast-1.0.0/database/human_gl_V -germline_db_J /usr/local/ncbi-igblast-1.0.0/database/human_gl_J -germline_db_D /usr/local/ncbi-igblast-1.0.0/database/human_gl_D -domain_system imgt -query $input -auxiliary_data /usr/local/ncbi-igblast-1.0.0/optional_file/human_gl.aux -show_translation -outfmt 3 > $output + </command> + <inputs> + <param name="input" type="data" format="fasta" label="Fasta file"/> + </inputs> + <outputs> + <data name="output" format="text" label="${input.name}-igBLASTn Report"/> + <!--<data name="log" format="text" label="log"/>--> + </outputs> + <requirements> + <requirement type="package" version="1.0.0">igBlastn</requirement> + </requirements> + <help> + there is no help + </help> +</tool>
--- a/tool_dependencies.xml Tue Sep 24 10:15:19 2013 -0400 +++ b/tool_dependencies.xml Tue Sep 24 10:42:31 2013 -0400 @@ -18,167 +18,16 @@ <action type="set_environment"> <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable> </action> - - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.ndm.imgt</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.ndm.kabat</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.pdm.imgt</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.pdm.kabat</action> - - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nhr</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nin</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nog</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsd</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsi</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsq</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.phr</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.pin</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.pog</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psd</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psi</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psq</action> - - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nhr</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nin</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nog</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsd</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsi</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsq</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.phr</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.pin</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.pog</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psd</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psi</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psq</action> - <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V_prot</action> <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action> <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action> - - <action type="move_file"> - <source>human_V</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.nhr</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.nin</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.nog</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.nsd</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.nsi</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.nsq</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.phr</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.pin</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.pog</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.psd</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.psi</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V.psq</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_V_prot</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - - - <action type="move_file"> - <source>human.ndm.imgt</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human.ndm.kabat</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human.pdm.imgt</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human.pdm.kabat</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - - <action type="move_file"> - <source>human_TR_V.nhr</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.nin</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.nog</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.nsd</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.nsi</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.nsq</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.phr</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.pin</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.pog</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.psd</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.psi</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - <action type="move_file"> - <source>human_TR_V.psq</source> - <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination> - </action> - + + <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/internal_data "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data"</action> + <action type="move_directory_files"> + <source_directory>internal_data</source_directory> + <destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</destination_directory> + </action> + </actions> </install> <readme>