Mercurial > repos > lparsons > htseq_count
changeset 9:971e20519fb8
Fix for dbkey column check when output additional bam is selected
| author | lparsons |
|---|---|
| date | Fri, 26 Oct 2012 15:57:08 -0400 |
| parents | 5bfb7a651fac |
| children | 5d969cb56112 |
| files | htseq-count.xml tool_dependencies.xml |
| diffstat | 2 files changed, 59 insertions(+), 59 deletions(-) [+] |
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--- a/htseq-count.xml Fri Sep 21 17:57:47 2012 -0400 +++ b/htseq-count.xml Fri Oct 26 15:57:08 2012 -0400 @@ -79,7 +79,7 @@ <when value="cached"> <param name="ref_file" type="select" label="Using reference genome"> <options from_data_table="sam_fa_indexes"> - <filter type="data_meta" key="dbkey" ref="samfile" column="3"/> + <filter type="data_meta" key="dbkey" ref="samfile" column="1"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param>
--- a/tool_dependencies.xml Fri Sep 21 17:57:47 2012 -0400 +++ b/tool_dependencies.xml Fri Oct 26 15:57:08 2012 -0400 @@ -1,58 +1,58 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="numpy" version="1.6.2"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> - <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> - - <package name="htseq" version="0.5.3p9"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> - <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. - </readme> - </package> - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> - </package> -</tool_dependency> +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.6.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> + + <package name="htseq" version="0.5.3p9"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. + </readme> + </package> + <package name="samtools" version="0.1.18"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> + <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>misc/maq2sam-long</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Compiling SAMtools requires the ncurses and zlib development libraries. + </readme> + </package> +</tool_dependency>