Mercurial > repos > pjbriggs > rnachipintegrator

comparison install_tool_deps.sh @ 0:0abe6bac47a6 draft

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planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
author pjbriggs
date Wed, 24 Feb 2016 09:25:18 -0500
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-1:000000000000 0:0abe6bac47a6
1 #!/bin/bash -e
2 #
3 # Install the tool dependencies for RnaChipIntegrator for testing from command line
4 #
5 # Installation directory
6 TOP_DIR=$1
7 if [ -z "$TOP_DIR" ] ; then
8 echo Usage: $(basename $0) DIR
9 exit
10 fi
11 if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
12 TOP_DIR=$(pwd)/$TOP_DIR
13 fi
14 if [ ! -d "$TOP_DIR" ] ; then
15 mkdir -p $TOP_DIR
16 fi
17 cd $TOP_DIR
18 # RnaChipIntegrator 1.0.0
19 VERSION=1.0.0
20 INSTALL_DIR=$TOP_DIR/rnachipintegrator/$VERSION
21 mkdir -p $INSTALL_DIR
22 wd=$(mktemp -d)
23 pushd $wd
24 wget https://pypi.python.org/packages/source/R/RnaChipIntegrator/RnaChipIntegrator-${VERSION}.tar.gz
25 tar zxf RnaChipIntegrator-${VERSION}.tar.gz
26 cd RnaChipIntegrator-$VERSION
27 pip install --no-use-wheel --install-option "--prefix=$INSTALL_DIR" .
28 popd
29 rm -rf $wd/*
30 rmdir $wd
31 cat > rnachipintegrator/$VERSION/env.sh <<EOF
32 #!/bin/sh
33 # Source this to setup rnachipintegrator/$VERSION
34 echo Setting up RnaChipIntegrator $VERSION
35 export PATH=$INSTALL_DIR/bin:\$PATH
36 export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
37 #
38 EOF
39 # xlsxwriter 0.8.4
40 INSTALL_DIR=$TOP_DIR/xlsxwriter/0.8.4
41 mkdir -p $INSTALL_DIR
42 wd=$(mktemp -d)
43 pushd $wd
44 wget -q https://pypi.python.org/packages/source/X/XlsxWriter/XlsxWriter-0.8.4.tar.gz
45 tar xzf XlsxWriter-0.8.4.tar.gz
46 cd XlsxWriter-0.8.4
47 OLD_PYTHONPATH=$PYTHONPATH
48 mkdir -p $INSTALL_DIR/lib/python
49 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python
50 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
51 popd
52 rm -rf $wd/*
53 rmdir $wd
54 export PYTHONPATH=$OLD_PYTHONPATH
55 cat > xlsxwriter/0.8.4/env.sh <<EOF
56 #!/bin/sh
57 # Source this to setup xlsxwriter/0.8.4
58 echo Setting up xlsxwriter 0.8.4
59 export PYTHONPATH=$INSTALL_DIR/lib/python:\$PYTHONPATH
60 export PATH=$INSTALL_DIR/bin:\$PATH
61 #
62 EOF
63 ##
64 #