RNA-seq issueshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues2021-03-05T11:07:23-06:00https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/123Handle image caching in CI better2021-03-05T11:07:23-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduHandle image caching in CI better`cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | xargs -P 3 -I {} bash -c "singularity pull --dir ${dir} 'docker://'{} || true"`
assumes:
- containers referred in nextflow.config are on docker hub and do not...`cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | xargs -P 3 -I {} bash -c "singularity pull --dir ${dir} 'docker://'{} || true"`
assumes:
- containers referred in nextflow.config are on docker hub and do not contain the "docker://" prefix
- containers referred in nextflow.config are prefixed by "container = " **EXACTLY** if a space is missing for example, that container will be skipped
need to make this more robustFUTURE Versionhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/117Update $31 snippet to use bash opt-args2021-03-19T18:05:50-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate $31 snippet to use bash opt-argsinstead of numbered inputsinstead of numbered inputsFUTURE VersionVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/94Update tracking db with on error2021-07-05T12:24:18-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate tracking db with on errorFUTURE Versionhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/93Add option for long lived globus-credential file2021-07-05T12:25:17-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd option for long lived globus-credential filein addition to current cookie and credential files
re Laura & Mike, servers set to require separate long-lived tokens, and deriva only keeps 1 long-lived token active
they are considering allowing multiple tokens to be active and if de...in addition to current cookie and credential files
re Laura & Mike, servers set to require separate long-lived tokens, and deriva only keeps 1 long-lived token active
they are considering allowing multiple tokens to be active and if decide to accept will be in another deriva update.
if they don't then long-lived token will work for production only runsFUTURE Versionhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/59Add new GRCm392021-04-20T21:59:50-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd new GRCm39FUTURE VersionVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/58AWS/DNANeuxs Cost2021-02-22T17:28:14-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAWS/DNANeuxs Cost*Currently in GUDMAP/RBK (20200723)*
607 current replicates
497 legacy "samples" (equivalent of replicates)
They want to migrate the legacy samples to be replicates, I don't know how much that has been done
worst case scenario is that 1...*Currently in GUDMAP/RBK (20200723)*
607 current replicates
497 legacy "samples" (equivalent of replicates)
They want to migrate the legacy samples to be replicates, I don't know how much that has been done
worst case scenario is that 1104 replicates to run...
20200722 test using AWS spot instances cost ~$0.984 for 1 PE replicate
20200723 test using AWS spot instances cost ~$0.012 for 1 PE replicate
***NEED TO TEST RUN WITH ON-DEMAND INSTANCES TO SEE WHAT MAX COST PER REPLICATE IS***FUTURE Versionhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/55Possibly move params.source to config?2021-07-05T12:22:52-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduPossibly move params.source to config?FUTURE Version