diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c53d8a46b173bcb46137bfb82348ba12e175626..14001f69b6bc50c8c1e0596fa2269cf34595c787 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,7 @@ **Background** * Corrected file search parameters due to name inconsistency (#129) +* Re-implemented sym-link for deriva cookie into ~/.bdbag/ for bdbag fetch to use (#132) # v2.0.0 **User Facing** diff --git a/README.md b/README.md index 7692cb70b453218bcf04ec31dd21ec0fcae7678c..1c505f9a8921d0202ec3dd620ca949f40c7ce2fd 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,13 @@ This pipeline was created to be a standard mRNA-sequencing analysis pipeline whi Authentication: ---------------- -The consortium server used must be authentificated with the [deriva authentication client](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/), and remain authentificated till the end of the pipeline run. Prematurely closing the client will result in invalidation of the tokens, and may result in the pipeline failure. The use of long-lived "globus" tokens is on the roadmap for use in the future. +The consortium server used must be authentificated with the [deriva authentication client](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/), and remain authentificated till the end of the pipeline run. Prematurely closing the client will result in invalidation of the tokens, and may result in the pipeline failure. The use of long-lived "globus" tokens is on the roadmap for use in the future. If you are using [v2.0.0](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tags/v2.0.0) you will be required to make a link for bdbag cookie. Below is the code to run: + +```sh +mkdir -p ~/.bdbag +ln -sf cookies.txt ~/.bdbag/deriva-cookies.txt +``` + To Run: ------- diff --git a/rna-seq.nf b/rna-seq.nf index 592c944c15e64702f5e63ba67e411737b3e11746..6073019182b2cb7f6ad5c6dd82fca011c58a0d95 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -206,7 +206,7 @@ process getBag { mkdir -p ~/.deriva ln -sf `readlink -e credential.json` ~/.deriva/credential.json echo -e "LOG: linked" >> ${repRID}.getBag.log - + # deriva-download replicate RID echo -e "LOG: fetching bag for ${repRID} in GUDMAP" >> ${repRID}.getBag.log deriva-download-cli ${source} --catalog 2 ${replicateExportConfig} . rid=${repRID} @@ -257,6 +257,13 @@ process getData { hostname > ${repRID}.getData.log ulimit -a >> ${repRID}.getData.log + # link deriva cookie for authentication + echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log + mkdir -p ~/.bdbag + ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt + echo -e "LOG: linked" >> ${repRID}.getData.log + + # get bag basename replicate=\$(basename "${inputBag}") echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log