Mercurial > repos > yhoogstrate > flaimapper
changeset 8:c5df479c423b draft
Uploaded
author | yhoogstrate |
---|---|
date | Thu, 19 Mar 2015 10:17:46 -0400 |
parents | 548e7c482077 |
children | 138748e037e4 |
files | README.md egg/flaimapper-1.1.2-py2.7.egg flaimapper.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
diffstat | 4 files changed, 43 insertions(+), 27 deletions(-) [+] |
line wrap: on
line diff
--- a/flaimapper.xml Fri Nov 07 10:54:58 2014 -0500 +++ b/flaimapper.xml Thu Mar 19 10:17:46 2015 -0400 @@ -1,39 +1,39 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper" name="FlaiMapper" version="1.1.0"> +<tool id="flaimapper" name="FlaiMapper" version="1.1.2.a"> <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> <requirements> - <requirement type="package" version="1.1.0">flaimapper</requirement> <requirement type="package" version="0.7.7">pysam</requirement> + <requirement type="package" version="0.8.1">pysam</requirement> + <requirement type="package" version="1.1.2">flaimapper</requirement> </requirements> + + <version_command>flaimapper --version</version_command> + <command> - ##rm $mask".tbi" - ##rm $fasta".fai" - flaimapper -v -f $output_format -o $output -m $mask -r $fasta - #for $alignment in $alignments - $alignment - #end for + + #for $alignment in $alignments + $alignment + #end for </command> - <version_command>flaimapper --version</version_command> - <inputs> <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" /> <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" /> - + <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> <param name="output_format" type="select" label="Output format"> - <option value="1">Tabular (1 fragment per column)</option> - <option value="2">Tabular (1 precursor per column)</option> - <option value="3">GenBank</option> - <!-- option value="gtf">GTF/GFF</option --> + <option value="1">Tabular (1 fragment per column)</option> + <option value="2">Tabular (1 precursor per column)</option> + <option value="3">GenBank</option> + <!-- option value="gtf">GTF/GFF</option --> </param> </inputs> @@ -42,6 +42,8 @@ </outputs> <help> + You must have 'easy_install' installed. + FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data doi:10.1093/bioinformatics/btu696
--- a/tool_data_table_conf.xml.sample Fri Nov 07 10:54:58 2014 -0500 +++ b/tool_data_table_conf.xml.sample Thu Mar 19 10:17:46 2015 -0400 @@ -1,8 +1,8 @@ <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> - <!-- Location of all GFF/GTF files --> - <table name="gene_sets" comment_char="#"> - <columns>name, dbkey, value, provider, reference</columns> - <file path="tool-data/gene_sets.loc" /> - </table> +<!-- Location of all GFF/GTF files --> +<table name="gene_sets" comment_char="#"> +<columns>name, dbkey, value, provider, reference</columns> +<file path="tool-data/gene_sets.loc" /> +</table> </tables> \ No newline at end of file
--- a/tool_dependencies.xml Fri Nov 07 10:54:58 2014 -0500 +++ b/tool_dependencies.xml Thu Mar 19 10:17:46 2015 -0400 @@ -1,19 +1,33 @@ <?xml version="1.0"?> <tool_dependency> <package name="pysam" version="0.7.7"> - <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="flaimapper" version="1.1.0"> + <package name="pysam" version="0.8.1"> + <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="flaimapper" version="1.1.2"> <install version="1.0"> <actions> - <action type="shell_command">git clone --quiet --recursive https://github.com/yhoogstrate/flaimapper.git ; cd flaimapper ; git reset --hard "109a7ee13cfad6eb4746422a5382a928e141d0a1" ; cd src ; python setup.py build</action><!-- 109a7ee13cfad6eb4746422a5382a928e141d0a1 should be the latest 1.1.0 commit --> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="make_directory">$INSTALL_DIR/lib64/python</action> - <action type="shell_command">cd src ; pwd ; ls ; export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + + <action type="set_environment_for_install"> + <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.7.7" /> + </repository> + <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.8.1" /> + </repository> + </action> + + <action type="make_directory">$INSTALL_DIR</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR:$INSTALL_DIR"/lib/python":$INSTALL_DIR"/lib64/python":$PYSAM_PATH:$PYSAM_PATH"/lib/python":$PYSAM_PATH"/lib64/python" ; easy_install --prefix=$INSTALL_DIR --install-dir=$INSTALL_DIR --script-dir=$INSTALL_DIR/bin $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.2-py2.7.egg"</action> <action type="set_environment"> - <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions>