Installed local Galaxy 24.0 on GCP Ubuntu 24.04. Galaxy submits jobs through pulsar to separate GCP instance[s] that run command-line tools. NCBI makeblastdb successfully generated nucleotide blastdb in Galaxy History – I see all 12 blastdb.n?? files, but when I run NCBI BLAST+ blastn tool against this blastdb in Galaxy history – it fails to stage / copy 12 blastdb.n??? generated by makeblastdb tool. It shows a single file – here is the command Galaxy ran:
gspier96@worker-6npw:/opt/pulsar/files/staging/278$ cat tool_script.sh
blastn -query ‘/opt/pulsar/files/staging/278/inputs/dataset_38b958dc-fefe-406f-ab17-7999e653898a.dat’ -db ‘/opt/pulsar/files/staging/278/inputs/dataset_6bc3f0f1-2c89-49f5-be1f-84de99a03580_files/blastdb’ …
gspier96@worker-6npw:/opt/pulsar/files/staging/278$ ls -l /opt/pulsar/files/staging/278/inputs/dataset_6bc3f0f1-2c89-49f5-be1f-84de99a03580_files/blastdb.*
-rw-rw-r–+ 1 pulsar pulsar 162 May 23 01:18 /opt/pulsar/files/staging/278/inputs/dataset_6bc3f0f1-2c89-49f5-be1f-84de99a03580_files/blastdb.ndb <<<< Only 1 / 12 blastdb.n?? files and it is gibberish:
gspier96@worker-6npw:/opt/pulsar/files/staging/278$ cat /opt/pulsar/files/staging/278/inputs/dataset_6bc3f0f1-2c89-49f5-be1f-84de99a03580_files/blastdb.ndb
403 Forbidden403 Forbidden
nginx/1.24.0 (Ubuntu)
What is the way[s] to configure pulsar to stage multiple files OR is there an alternative way to resolve this issue? NCBI_blastn vs. shared blastdb (not in Galaxy History) works fine.
Thanks you! - Gene Spier gspier96@gmail.com