This is in regards to a local install deployment on CentOS 7 with Python 2.7.5 - an update and a question.
In order to get the run.sh & common_startup scripts to work I had to modify the common_startup to prevent SSL issues:
: ${GALAXY_WHEELS_INDEX_URL:="http://wheels.galaxyproject.org/"} <--changed this from https to http
if [ $REPLACE_PIP -eq 1 ]; then pip install 'pip>=8.1' fi
Added this -> : ${GALAXY_TRUST_HOST:="wheels.galaxyproject.org"}
if [ $FETCH_WHEELS -eq 1 ]; then pip install -r requirements.txt --extra-index-url ${GALAXY_WHEELS_INDEX_URL} --trusted-host ${GALAXY_TRUST_HOST} <--Added this
This is effectively allows you to do install the with following command line: pip install --upgrade --extra-index-url http://wheels.galaxyproject.org/ --trusted-host wheels.galaxyproject.org <package>
This works until you get to the pysam package listed in the requirements.txt file: pysam==0.8.4+gx1
The following error manifests: Collecting pysam==0.8.4+gx1 (from -r requirements.txt (line 69)) Could not find a version that satisfies the requirement pysam==0.8.4+gx1 (from -r requireme nts.txt (line 69)) (from versions: 0.4, 0.4.1, 0.7.6, 0.7.7, 0.7.8, 0.8.0, 0.8.1, 0.8.2, 0.8. 2.1, 0.8.3, 0.8.4, 0.9.0, 0.9.1, 0.9.1.1, 0.9.1.2, 0.9.1.3) No matching distribution found for pysam==0.8.4+gx1 (from -r requirements.txt (line 69))
This package is installed, but not from the galaxy repo: [root@galaxy1 scripts]# pip install pysam Requirement already satisfied (use --upgrade to upgrade): pysam in /usr/lib64/python2.7/site-packages
Any ideas how to get past this issue? Thanks