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churchlab
/
millstone
Genome engineering and analysis software
http://churchlab.github.io/millstone/
MIT License
47
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Bump numpy from 1.8.1 to 1.22.0 in /requirements
#713
dependabot[bot]
opened
2 years ago
0
Bump numpy from 1.8.1 to 1.21.0 in /requirements
#712
dependabot[bot]
closed
2 years ago
1
ALIGNMENT PIPELINE ERROR
#711
seamyname
opened
2 years ago
2
Bump ipython from 0.13.2 to 7.16.3 in /requirements
#710
dependabot[bot]
opened
2 years ago
0
Bump celery from 3.1.17 to 5.2.2 in /requirements
#709
dependabot[bot]
opened
2 years ago
0
Bump django from 1.5.1 to 2.2.24 in /requirements
#708
dependabot[bot]
opened
3 years ago
0
Bump django-registration from 1.0 to 3.1.2 in /requirements
#707
dependabot[bot]
opened
3 years ago
0
Bump django from 1.5.1 to 1.11.29 in /requirements
#706
dependabot[bot]
closed
3 years ago
1
Bump django from 1.5.1 to 1.11.28 in /requirements
#705
dependabot[bot]
closed
4 years ago
1
Will you be updating to Python 3?
#704
Zymergen-phaverty
closed
4 years ago
1
Is there any interactive/guided in-depth tutorial available?
#703
WizardOfAus
closed
4 years ago
1
Bump django from 1.5.1 to 1.11.23 in /requirements
#702
dependabot[bot]
closed
4 years ago
1
Problem uploading samples
#701
Zymergen-SBRUBAKER
opened
4 years ago
36
Files uploaded through browser remain in /tmp after completion
#700
glebkuznetsov
opened
6 years ago
0
Generate New Reference Genome: ERROR: More than one record found in handle
#699
bfurtwa
opened
6 years ago
5
How is extremely high-coverage defined?
#698
bfurtwa
opened
6 years ago
1
Fix broken dependency binary links
#697
glebkuznetsov
closed
6 years ago
0
jbrowse contig fail
#696
MaxSchubert
opened
6 years ago
0
filter key Gene non-functional
#695
MaxSchubert
opened
6 years ago
0
Genbank exported from latest version of Geneious appears to cause error
#694
glebkuznetsov
opened
7 years ago
0
Scaffold command for dropping materialized view indices.
#693
glebkuznetsov
closed
7 years ago
0
Temporary force travis-ci to use old machines.
#692
glebkuznetsov
closed
7 years ago
0
OptMAGE only works with MG1655
#691
dbgoodman
opened
7 years ago
0
OptMAGE support doesn't work for multi-bp SNVs
#690
dbgoodman
opened
7 years ago
0
Jbrowse tracks for deleted alignments get left behind
#689
dbgoodman
opened
7 years ago
0
Make queries be case insensitive
#688
dbgoodman
opened
8 years ago
0
Velvetg runs out of memory during graph building
#687
glebkuznetsov
opened
8 years ago
0
Contig calling shows QUEUED_TO_ASSEMBLE even though really ASSEMBLING, sometimes.
#686
glebkuznetsov
opened
8 years ago
0
JBrowse warning when re-running contig pipeline
#685
glebkuznetsov
opened
8 years ago
2
In pre-contig run cleanup, delete old error reports?
#684
glebkuznetsov
closed
8 years ago
1
On variant csv export, what to do about LONG REF/ALT alleles?
#683
dbgoodman
opened
8 years ago
0
Contig assembly on bootstrap data fails
#682
glebkuznetsov
closed
8 years ago
1
No UI feedback on starting contig assembly
#681
glebkuznetsov
closed
8 years ago
0
Running some java dependencies (i.e. snpeff) with Java1.6 (Apple Java) causes failures.
#680
dbgoodman
closed
8 years ago
1
Unsupported Variant filter query EXPERIMENT_SAMPLE_LABEL = "C-E4-2”
#679
glebkuznetsov
closed
8 years ago
0
Old assemblies aren't deleted
#678
dbgoodman
closed
8 years ago
1
If materialization is kicked off from the variant view UI, and page is refreshes, materialization happens again and they collide.
#677
dbgoodman
opened
8 years ago
3
Look into custom SV calling pipeline parallelization.
#676
glebkuznetsov
opened
8 years ago
0
Mobile Element finding crashes when contigs are identified across two IS elements
#675
dbgoodman
opened
8 years ago
0
Latest SV pipeline fixes 2016 05 30
#674
glebkuznetsov
closed
8 years ago
0
Make SVs from Brian's Pipeline flip the IS_SV flag
#673
dbgoodman
opened
8 years ago
0
Annotation on SVs (maybe SnpEff?)
#672
glebkuznetsov
opened
8 years ago
0
Need to be more stringent when calling deletions using low coverage
#671
glebkuznetsov
opened
8 years ago
1
Can't start calling contigs for all samples if > 10 (view page size) contigs
#670
glebkuznetsov
closed
8 years ago
3
Millstone does not like certain .gb template files, throws "next iteration" error
#669
mnapolitano89
opened
8 years ago
2
Millstone not collecting unused reads for contig assembly use
#668
mnapolitano89
opened
8 years ago
4
Make SnpEff an option the user can control
#667
glebkuznetsov
opened
8 years ago
0
if contig assembler errors out, it does not change status from assembling to error or throw a user visable error
#666
mnapolitano89
opened
8 years ago
0
calling "call sv using assembled contigs" before contigs finished assembling causes assembly to fail
#665
mnapolitano89
closed
8 years ago
1
for multiple chromosome alignments, group by chromosome and not by position
#664
mnapolitano89
closed
8 years ago
1
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