Closed donkirkby closed 10 years ago
Since I'm probably going to do this many times, I will record the configuration steps here. They're based on the instructions in INSTALL.md.
cd ~/git/Shipyard/shipyard
python manage.py shell
from librarian.models import SymbolicDataset
from django.contrib.auth.models import User
u = User.objects.get(username='shipyard')
SymbolicDataset.create_SD('/mnt/data/don/data/RAW_DATA/140522/46824A-3515-HLA-B-E99601CLIMX-PR-RT_S23_L001_R1_001.fastq', user=u, name='46824A-3515-HLA-B-E99601CLIMX-PR-RT_S23_L001_R1_001.fastq', description='example FASTQ, forward read')
SymbolicDataset.create_SD('/mnt/data/don/data/RAW_DATA/140522/46824A-3515-HLA-B-E99601CLIMX-PR-RT_S23_L001_R2_001.fastq', user=u, name='46824A-3515-HLA-B-E99601CLIMX-PR-RT_S23_L001_R2_001.fastq', description='example FASTQ, reverse read')
SymbolicDataset.create_SD('/home/don/git/MiseqPipeline/reference_sequences/cfe.fasta', user=u, name='cfe.fasta', description='initial set of references in FASTA format')
SymbolicDataset.create_SD('/home/don/git/MiseqPipeline/reference_sequences/csf2counts_amino_refseqs.csv', user=u, name='csf2counts_amino_refseqs.csv', description='amino acid reference sequences')
exit()
settings.py
, hyphyAlign.py
, prelim_map.py
, remap.py
, sam2csf.py
, csf2counts.py
. Copy the description from each script's help text, and add a dependency on settings.py
to all the other code resources, except hyphyAlign.py
. csf2counts.py
also needs a dependency on hyphyAlign.py
. Leave each dependency's path blank, and use a filename of settings.py
or hyphyAlign.py
.I successfully ran the MiSeq pipeline under Shipyard for a single sample. Woot! I had to hack around a couple of bugs to make it work, so I will record those as issues tomorrow before closing this issue.
Sweet!
On Jun 17, 2014, at 5:05 PM, Don Kirkby wrote:
I successfully ran the MiSeq pipeline under Shipyard for a single sample. Woot! I had to hack around a couple of bugs to make it work, so I will record those as issues tomorrow before closing this issue.
— Reply to this email directly or view it on GitHub.
The outstanding issues are #125 and #126, but this issue can close.
This task is to check out the shipyard branch of the MiSeq pipeline project, set up all the configuration, and run the pipeline on a developer workstation for an example FASTQ file.