HTSeq: fix 0.8.0 and add 0.9.0

apps/HTSeq/install_0.8.0.sh

@@ -34,11 +34,11 @@
 # knowledge of the CeCILL license and that you accept its terms.
 
 source ../build_env.sh
-module load python/2.7.13
+module load Python/2.7.13
 
 HTSEQ_VERSION=0.8.0
 PYSAM_VERSION=0.11.2.2
-HTSEQ_ROOT=/Xnfs/lbmcdb/common/modules/apps/HTSeq/${HTSEQ_VERSION}
+HTSEQ_ROOT=/Xnfs/lbmcdb/common/modules/apps/HTSeq/${HTSEQ_VERSION}/
 mkdir -p ${HTSEQ_VERSION}/lib/python2.7/dist-packages/
 PYTHONPATH=$PYTHONPATH:${HTSEQ_ROOT}/lib/python2.7/dist-packages/
 
@@ -52,5 +52,6 @@ git clone https://github.com/simon-anders/htseq.git
 cd htseq
 git checkout tags/release_${HTSEQ_VERSION}
 python setup.py install --single-version-externally-managed --prefix ${HTSEQ_ROOT} --record htseq_install.txt
+cd ..
 
 rm -Rf htseq pysam

apps/HTSeq/install_0.9.1.sh

+#!/bin/bash
+# Copyright laurent modolo for the LBMC UMR 5239 ©.
+# contributor(s) : laurent modolo (2017)
+#
+# laurent.modolo@ens-lyon.fr
+#
+# This software is a computer program whose purpose is to manage dated file
+# names in complience with the bioinformatic good practices used in the LBMC.
+#
+# This software is governed by the CeCILL  license under French law and
+# abiding by the rules of distribution of free software.  You can  use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and,  more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+source ../build_env.sh
+module load Python/2.7.13
+
+HTSEQ_VERSION=0.9.1
+PYSAM_VERSION=0.11.2.2
+HTSEQ_ROOT=/Xnfs/lbmcdb/common/modules/apps/HTSeq/${HTSEQ_VERSION}/
+mkdir -p ${HTSEQ_VERSION}/lib/python2.7/dist-packages/
+PYTHONPATH=$PYTHONPATH:${HTSEQ_ROOT}/lib/python2.7/dist-packages/
+
+git clone https://github.com/pysam-developers/pysam.git
+cd pysam
+git checkout tags/v${PYSAM_VERSION}
+python setup.py install --single-version-externally-managed --prefix ${HTSEQ_ROOT} --record pysam_install.txt
+cd ..
+
+git clone https://github.com/simon-anders/htseq.git
+cd htseq
+git checkout tags/release_${HTSEQ_VERSION}
+python setup.py install --single-version-externally-managed --prefix ${HTSEQ_ROOT} --record htseq_install.txt
+cd ..
+
+rm -Rf htseq pysam

modulefiles/HTSeq/0.8.0.lua

@@ -35,7 +35,7 @@ knowledge of the CeCILL license and that you accept its terms.
 --]=====]
 
 local root = "/Xnfs/lbmcdb/common/modules/apps/HTSeq/0.8.0"
-conflict("file_handle")
+conflict("HTSeq")
 conflict("Python/3.6.1")
 load("Python/2.7.13")
 prereq_any("Python/2.7.13")

modulefiles/HTSeq/0.9.0.lua

+--[=====[
+Copyright laurent modolo for the LBMC UMR 5239 ©.
+contributor(s) : laurent modolo (2017)
+
+laurent.modolo@ens-lyon.fr
+
+This software is a computer program whose purpose is to manage dated file
+names in complience with the bioinformatic good practices used in the LBMC.
+
+This software is governed by the CeCILL  license under French law and
+abiding by the rules of distribution of free software.  You can  use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and  rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty  and the software's author,  the holder of the
+economic rights,  and the successive licensors  have only  limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean  that it is complicated to manipulate,  and  that  also
+therefore means  that it is reserved for developers  and  experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and,  more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+--]=====]
+
+local root = "/Xnfs/lbmcdb/common/modules/apps/HTSeq/0.9.0"
+conflict("HTSeq")
+conflict("Python/3.6.1")
+load("Python/2.7.13")
+prereq_any("Python/2.7.13")
+prepend_path{"PATH", pathJoin(root, "bin")}
+setenv("HTSEQ_PATH", pathJoin(root, "bin"))