Mercurial > repos > yhoogstrate > flaimapper
changeset 19:ab3ea877607f draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Fri, 20 Mar 2015 11:14:32 -0400 |
| parents | 0e9520cf7587 |
| children | ac69be28e786 |
| files | README.rst egg/flaimapper-1.1.4-py2.7.egg egg/flaimapper-1.1.5-py2.7.egg flaimapper.xml tool_dependencies.xml |
| diffstat | 5 files changed, 22 insertions(+), 7 deletions(-) [+] |
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--- a/README.rst Fri Mar 20 10:45:21 2015 -0400 +++ b/README.rst Fri Mar 20 11:14:32 2015 -0400 @@ -29,7 +29,7 @@ **pysam**: -The MIT License (>=3) +The MIT License References ----------
--- a/flaimapper.xml Fri Mar 20 10:45:21 2015 -0400 +++ b/flaimapper.xml Fri Mar 20 11:14:32 2015 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper" name="FlaiMapper" version="1.1.4.a"> +<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a"> <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> <requirements> - <requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! --> - <requirement type="package" version="1.1.4">flaimapper</requirement> + <requirement type="package" version="0.8.2.1">pysam</requirement> + <requirement type="package" version="1.1.5">flaimapper</requirement> </requirements> <version_command>flaimapper --version</version_command> @@ -62,6 +62,21 @@ The reference sequence should be provided in FASTSA format. +You can access **ncRNAdb09** at the following URLs: +https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* +https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* + +Therefore you need bam files aligned to the same reference. We have made +the following available: + + - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz + - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz + +If you want to test flaimapper with example data you can obtain several +alignment files from this following directory tree: + +https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments + Installation ------------ @@ -77,7 +92,7 @@ **pysam**: -The MIT License (>=3) +The MIT License Contact -------
--- a/tool_dependencies.xml Fri Mar 20 10:45:21 2015 -0400 +++ b/tool_dependencies.xml Fri Mar 20 11:14:32 2015 -0400 @@ -4,7 +4,7 @@ <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="flaimapper" version="1.1.4"> + <package name="flaimapper" version="1.1.5"> <install version="1.0"> <actions> @@ -17,7 +17,7 @@ <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 $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.4-py2.7.egg"</action> + <action type="shell_command">export PYTHONPATH=$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 $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.5-py2.7.egg"</action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>