diff --git a/docs/Software_installation.md b/docs/Software_installation.md index ac856264e9eadc1fd4b33b6d13e5d469f70847b7..41013554bc3c00cc3a5d59512f7a5a8982768acc 100644 --- a/docs/Software_installation.md +++ b/docs/Software_installation.md @@ -114,31 +114,22 @@ mv /home/u035/project/software/install/1000G_phase3_hg38/1000g.phase3.100k.b38* ## Python modules -Users should include this line in any shell scripts requiring these modules, and ensure this command is run prior to installing any Python modules in this location. - -``` -export PYTHONPATH=/home/u035/project/software/lib/python3.6/site-packages -``` - ### VASE -VASE was installed following the instructions at https://github.com/david-a-parry/vase, downloaded 27 August 2020. +VASE v0.4 was installed 28 August 2020. ``` -cd /home/u035/project/software/install -git clone https://github.com/david-a-parry/vase.git -cd vase -/home/u035/project/software/bcbio/anaconda/bin/python3 setup.py install --prefix /home/u035/project/software +cd /home/u035/project/software +./bcbio/anaconda/bin/pip3 install git+git://github.com/david-a-parry/vase.git#egg=project[BGZIP,REPORTER,MYGENE] ``` ### XlsxWriter +XlsxWriter 1.3.3 was installed 28 August 2020. + ``` -cd /home/u035/project/software/install -git clone https://github.com/jmcnamara/XlsxWriter.git -cd XlsxWriter -/home/u035/project/software/bcbio/anaconda/bin/python3 setup.py install --prefix /home/u035/project/software -rsync -av xlsxwriter ../../lib/python3.6/site-packages +cd /home/u035/project/software +./bcbio/anaconda/bin/pip3 install XlsxWriter ``` ## GATK 3.8