the-sequence-ontology / gal Goto Github PK

On Sep 19, 2017, at 2:40 AM, Philippe Grevet [email protected] wrote:

Hello,

I want to compile GAL
on server Debian jessie
all prerequise seem good,
but :

#perl ./Build.PL --prefix /scratch/DEPOT/INSTALL/GAL/
WARNING: the following files are missing in your kit:
t/data/augustus_short.gff3
t/data/binary_search_test.txt
t/data/chip_all.sam
t/data/cufflinks_short.gff3
t/data/fasta_hg18/directory.index
t/data/Homo_sapiens.GRCh37.73.chr22.short.gff3
Please inform the author.

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GAL' version 'v0.2.1'

#./Build
Building GAL
All prerequisites satisfied

#./Build testall > ../Build-testall-GAL-version-v0.2.1.log 2>&1

I join the log file

Where is the problem ?
Thanks
Best regards

Hi,

I've ended up here after failed attempts to download GAL library from http://www.sequenceontology.org/software/GAL.html

For the sake of fellow researchers could you add links / make the download link to redirect here?

Best regards

Hi,
I try to use docker run and docker exec for GAL.
The two commands are :

1. docker run -dit --name 174 -v /local/directory/:/usr/GAL_data
2. docker exec 174 python3 /usr/GAL/gal_manage.py --orconfig=/usr/GAL_data/111.ini

In a terminal, when I separately run the two commands one by one, they both work.

However, when I write them in a shell script and run the shell script, the command "docker exec..." always does not work. The errors shown out is:

4a603795c15dfd53a37ea9dee142816c584237f2e277136284fb1cdce1f83236
GAL Upload started

Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pymysql/connections.py", line 920, in connect
**kwargs)
File "/usr/lib/python3.6/socket.py", line 724, in create_connection
raise err
File "/usr/lib/python3.6/socket.py", line 713, in create_connection
sock.connect(sa)
OSError: [Errno 99] Cannot assign requested address

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/GAL/gal_manage.py", line 24, in
main.process_schema_common_data(db_config, arg, CurrDir)
File "/usr/GAL/main.py", line 85, in process_schema_common_data
db_function.check_db_connection(db_config.host, db_config.db_username, db_config.db_password)
File "/usr/GAL/galpy/db_function.py", line 100, in check_db_connection
db = pymysql.connect(host, db_username, db_password)
File "/usr/lib/python3/dist-packages/pymysql/init.py", line 90, in Connect
return Connection(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pymysql/connections.py", line 699, in init
self.connect()
File "/usr/lib/python3/dist-packages/pymysql/connections.py", line 967, in connect
raise exc
pymysql.err.OperationalError: (2003, "Can't connect to MySQL server on 'localhost' ([Errno 99] Cannot assign requested address)")

In the Synopsis:

• Where it says:
  ` --rev_comp

  Reverse compliment a sequence.  Same as --rev_seq && --comp_seq
  together.
  

`

• It should say:
  `
  --rev_comp

  Reverse complement a sequence.  Same as --rev_seq && --comp_seq
  together.
  

`

• Where it says:
  --filter_horter Filter (remove) entries shorter than the filter. IE "--filter_shorter 800" will filter all sequences <= 800 basepairs long.

• It should say:
  --filter_shorter Filter (remove) entries shorter than the filter. IE "--filter_shorter 800" will filter all sequences <= 800 basepairs long.

• Thanks!

• After installing in both Ubuntu and MacOS, I do not get any errors, but tyhe following warnings:

perl Build.PL
WARNING: the following files are missing in your kit:
t/data/augustus_short.gff3
t/data/binary_search_test.txt
t/data/chip_all.sam
t/data/cufflinks_short.gff3
t/data/fasta_hg18/directory.index
t/data/Homo_sapiens.GRCh37.73.chr22.short.gff3
Please inform the author.

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GAL' version "v0.2.1"

• So I am informing the author...
• I assume these are test files too large to be included in GitHub??
• If the above is true, then I would like to suggest to deploy those files in Zenodo, so that they can be downloaded??. Thanks

Line 1994 of the SO GVF validator, gvf_validator.pl, uses the obsolete page:

http://www.sequenceontology.org/resources/obo_files/current_release.obo

It should be updated to use the following page instead:

https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so-xp.obo

This is being opened to replace The-Sequence-Ontology/SO-Ontologies#365, which will be closed.