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medema-group / bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
GNU Affero General Public License v3.0
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[Feature Request] Remove the requirement for the output directory to have a subdirectory called `result` (even in a new run) #66

Open jolespin opened 1 year ago

jolespin commented 1 year ago 
(VEBA-biosynthetic_env) [jespinoz@exp-15-01 Test]$ bigslice --query  test_output/biosynthetic/intermediate/1__antismash/SRR17458614__CONCOCT__P.2__9/ --query_name SRR17458614__CONCOCT__P.2__9 --program_db_folder /expanse/projects/jcl110/db/veba/VDB_v4/Annotate/BiG-SLiCE/ bigslice_output
Output folder didn't exists!
BiG-SLiCE run failed.

DIRECTORY=bigslice_output
(VEBA-biosynthetic_env) [jespinoz@exp-15-01 Test]$ if [ -d "$DIRECTORY" ]; then echo "$DIRECTORY does exist."; fi
bigslice_output does exist.

I'm not sure how to get this to run. I've made sure the input directory exists, the output directory exists, and the database is specified.

Here's the line: https://github.com/medema-group/bigslice/blob/e11b979dbc5c3acaa067f5012d2d08da5c01dd76/bigslice/bigslice#L1009

Side note: It might be useful to not require the database path to check the version

(VEBA-biosynthetic_env) [jespinoz@exp-15-01 Test]$ bigslice --version
Can't find HMM model libraries!
BiG-SLiCE run failed.

(VEBA-biosynthetic_env) [jespinoz@exp-15-15 TestVEBA]$ conda list | grep "bigslice"
bigslice                  1.1.1                    pypi_0    pypi
jolespin commented 1 year ago

Figured it out. The output folder MUST have a subdirectory called result https://github.com/medema-group/bigslice/blob/e11b979dbc5c3acaa067f5012d2d08da5c01dd76/bigslice/bigslice#L952

In future updates, can the output directory be sufficient instead of output_directory/result ?

Now I'm getting this error: 

(VEBA-biosynthetic_env) [jespinoz@exp-15-15 Test]$ bigslice --query  test_output/biosynthetic/intermediate/1__antismash/SRR17458614__CONCOCT__P.2__9/ --query_name SRR17458614__CONCOCT__P.2__9 --program_db_folder /expanse/projects/jcl110/db/veba/VDB_v4/Annotate/BiG-SLiCE/ bigslice_output
pid 1058573's current affinity list: 110
pid 1058573's new affinity list: 110
pid 1058570's current affinity list: 110
pid 1058570's new affinity list: 110
Fetching run details...
Can't find a matching hmm library in the database!
BiG-SLiCE run failed.