Usage: the init command - not working

ElitaJaun commented 5 years ago

Dear Florent,

I am not able to run the example of pantagruel usage as given: pantagruel -d databasename -r /root/folder/for/database -f PANTAGFAM -I email -A /folder/of/public/genome/in/RefSeq/format init

I ran:

$ pantagruel -d test -r ./ -f PANTAGFAM -I e.jauneikaite@imperial.ac.uk -A GCF_000007265.1_ASM726v1/ init

but got the following error:

set gene family prefix to 'PANTAGFAM'
set identity to 'e.jauneikaite@imperial.ac.uk'
set NCBI RefSeq(-like) genome assembly source folder to 'GCF_000007265.1_ASM726v1/'
will create/use Pantagruel database 'test', set in root folder: './'

will run tasks: init
[2019-02-22 14:37:09] Pantagrel pipeline step init: initiate pangenome database.
/home/elita/pantagruel_pipeline/pantagruel/scripts/pipeline/pantagruel_pipeline_master.sh: line 472: setdefaults: command not found
/home/elita/pantagruel_pipeline/pantagruel/scripts/pipeline/pantagruel_pipeline_master.sh: line 473: /scripts/pipeline/pantagruel_pipeline_init.sh: No such file or directory
ERROR:

How could I check that I have all the required commands/scripts installed correctly?

Thank you. Bw, Elita

flass commented 5 years ago

Hi Elita, thanks for the bug reports.

about the bug relative to setdefaults; there was a syntax error, fixed in commits 4c90719 and 37bd608.
the bug relative to not finding the script was due to you not specifying the hard path to the Pantagruel code repository through -p option. This option seemed rather a source of confusion to the program than anything useful, I removed it (commit 478057f) and fixed the automatic detection of the code repository path (commits 478057f and c93ef2e).
Also I noticed you were using relative paths for various arguments, and made the master script robust to relative path in input arguments (commit 3177cd9).
In addition, I see you are specifying a single assembly folder as value for option -A. This is not the correct syntax: you have to provide a folder that contains folder(s) of assemblies (cf. description of input in README).
Finally, you need to provide a minimum of 4 genomes, or Pantagruel will return an error in task 00. I clarified these last two point in the README (commit a024d9e).

I tested init task with your command and it should work fine (as for commit 66f1f27). Please let me know if anything else goes wrong.

Cheers, Florent

ElitaJaun commented 5 years ago

Hi Florent, Thank you - it all works now. Bw, Elita

flass commented 5 years ago

Great, thanks for reporting.

flass / pantagruel

Usage: the init command - not working #4