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Commit 0d27c13d authored by ameyner2's avatar ameyner2
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Update python modules installation.

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docs/Software_installation.md
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...@@ -114,31 +114,22 @@ mv /home/u035/project/software/install/1000G_phase3_hg38/1000g.phase3.100k.b38* ...@@ -114,31 +114,22 @@ mv /home/u035/project/software/install/1000G_phase3_hg38/1000g.phase3.100k.b38*
## Python modules ## 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
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 cd /home/u035/project/software
git clone https://github.com/david-a-parry/vase.git ./bcbio/anaconda/bin/pip3 install git+git://github.com/david-a-parry/vase.git#egg=project[BGZIP,REPORTER,MYGENE]
cd vase
/home/u035/project/software/bcbio/anaconda/bin/python3 setup.py install --prefix /home/u035/project/software
``` ```
### XlsxWriter ### XlsxWriter
XlsxWriter 1.3.3 was installed 28 August 2020.
``` ```
cd /home/u035/project/software/install cd /home/u035/project/software
git clone https://github.com/jmcnamara/XlsxWriter.git ./bcbio/anaconda/bin/pip3 install XlsxWriter
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
``` ```
## GATK 3.8 ## GATK 3.8
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