Specify software versions

[shntnu]

We should specify software versions

Cloned repos

grep -A 2 -B 2 -n "git clone" *.md
02-config.md-88-mkdir software
02-config.md-89-cd software
02-config.md:90:git clone https://github.com/broadinstitute/pe2loaddata.git
02-config.md:91:git clone https://github.com/CellProfiler/Distributed-CellProfiler.git
02-config.md-92-
02-config.md-93-cd ..
--
05-create-profiles.md-67-if [ -d pycytominer ]; then rm -rf pycytominer; fi
05-create-profiles.md-68-
05-create-profiles.md:69:git clone https://github.com/cytomining/pycytominer.git
05-create-profiles.md-70-
05-create-profiles.md-71-cd pycytominer

For cytominer-database, keep this issue in mind: https://stackoverflowteams.com/c/broad-institute-imaging-platform/questions/96 i.e. need to peg pandas<2.1.4

Other

• CellProfiler: should be compatible with whatever version we specify for Distributed-CellProfiler

We needn't specify these versions because they are pegged via the AMI, but we should point to the versions used in the AMI

• Python
• awscli
• Miniconda