Mercurial > repos > yhoogstrate > package_flaimapper_1_2_1
changeset 0:88696b8f774b draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_flaimapper_1_2_1 commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty
| author | yhoogstrate |
|---|---|
| date | Wed, 03 Jun 2015 07:56:49 -0400 |
| parents | |
| children | 6262f77f889a |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 60 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 03 07:56:49 2015 -0400 @@ -0,0 +1,60 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- + pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 & + 0.8.3 and therefore FlaiMapper is not compatible with all of + them. For compatibility this package is provided with pysam + 0.8.2.1 which was not originally in the toolshed. + --> + <package name="pysam" version="0.8.2.1"> + <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="flaimapper" version="1.2.1"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.8.2.1" /> + </repository> + </action> + + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="make_directory">$INSTALL_DIR/lib64/python</action> + + <action type="shell_command"> + git clone https://github.com/yhoogstrate/flaimapper flaimapper && + cd flaimapper && + git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779 && + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR && + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python" && + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python" && + export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH && + export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python" && + export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python" && + + cd src && + + python setup.py build && + python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin + </action> + + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$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> + </install> + + <readme> + Downloads and installs FlaiMapper. Prerequisites: + - git + + Because I accidentally included too much large files within + the GitHub repository of FlaiMapper it has become large. + This explains why installation takes a while. + </readme> + </package> +</tool_dependency>