forked from PacificBiosciences/pbcommand
/
bamboo_build.sh
executable file
·29 lines (25 loc) · 1.13 KB
/
bamboo_build.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
#!/bin/bash -ex
NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-4.9.2
export PATH=$PWD/bin:/mnt/software/a/anaconda2/4.2.0/bin:$PATH
export PYTHONUSERBASE=$PWD
export CFLAGS="-I/mnt/software/a/anaconda2/4.2.0/include"
PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"
type module >& /dev/null || . /mnt/software/Modules/current/init/bash
module load gcc/4.9.2
rm -rf bin lib include share
mkdir bin lib include share
$PIP install --user \
iso8601
$PIP install --user \
$NX3PBASEURL/pythonpkgs/xmlbuilder-1.0-cp27-none-any.whl \
$NX3PBASEURL/pythonpkgs/tabulate-0.7.5-cp27-none-any.whl \
$NX3PBASEURL/pythonpkgs/pysam-0.9.1.4-cp27-cp27mu-linux_x86_64.whl \
$NX3PBASEURL/pythonpkgs/avro-1.7.7-cp27-none-any.whl
$PIP install --user --upgrade "pylint<2.0.0"
$PIP install --user -r REQUIREMENTS.txt
$PIP install --user -r REQUIREMENTS_TEST.txt
$PIP install --user -e ./
nosetests -s --verbose --with-xunit --xunit-file=nosetests.xml --with-coverage --cover-xml --cover-xml-file=coverage.xml --logging-config \
log_nose.cfg tests/test_*.py
sed -i -e 's@filename="@filename="./@g' coverage.xml
make run-pylint run-pep8