Comments (3)
r06942072
commented on May 27, 2024
Checklist (I take organism honeybee as an example)
*addorganism
- python manage.py addorganism Apis mellifera
*addblast
- python manage.py addblast Apis mellifera -t peptide protein -f GCF_003254395.2_Amel_HAv3.1_genomic.fna
*makeblastdb
- python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -m
*populatesequence
- python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -p
*addhmmer
- python manage.py addhmmer Apis mellifera -f GCF_003254395.2_Amel_HAv3.1_genomic.fna
*delete
-
python manage.py delete -o Apis mellifera
-
python manage.py delete -b GCF_003254395.2_Amel_HAv3.1_genomic.fna
-
python manage.py delete -h
GCF_003254395.2_Amel_HAv3.1_genomic.fna
from genomics-workspace.
r06942072
commented on May 27, 2024
merge branch addorg3 into master branch.
addorg3 add 5 more commands :
Checklist (I take organism honeybee as an example)
*addorganism
- python manage.py addorganism Apis mellifera
*addblast
- python manage.py addblast Apis mellifera -t peptide protein -f GCF_003254395.2_Amel_HAv3.1_genomic.fna
*makeblastdb
- python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -m
*populatesequence
- python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -p
*addhmmer
- python manage.py addhmmer Apis mellifera -f GCF_003254395.2_Amel_HAv3.1_genomic.fna
from genomics-workspace.
mpoelchau
commented on May 27, 2024
Great!
- Documentation in readthedocs still needs to be updated
- function delete is in addorg2 - we'll need to set up a PR and test
from genomics-workspace.
Related Issues (20)
- Re-written [BLAST query page] by React JS library HOT 5
- [BLAST query page] Organism display order HOT 1
- Final step to Integrate the adding organism functionality to CWL and fix CI issue HOT 3
- Do we need the sequences table? HOT 1
- Adding delete feature to script HOT 2
- Test if linkouts appear when ENABLE_JBROWSE_INTEGRATION = False HOT 1
- add CLI function to set is_shown HOT 3
- The blast_sequence table is big and only getting bigger HOT 10
- Moving docker version to the new repo
- vulnerabilities of django 1.11.20 and update blastdbcmd argument HOT 3
- Update readthedocs with command line interface documentation
- Consider truncating BLAST results when they are too large
- manage.py addOrganism capitalizes the short_name entry
- Using dbtitle in blast-results.js is awkward
- disable travis CI HOT 1
- Problems with multiple space characters in organism name
- google analytics code is missing
- change draggableBlastFeature to draggableNeatBlastFeature HOT 1
- Add Apollo link-outs to transcript and protein features HOT 1
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