churchlab millstone issues

churchlab / millstone

Genome engineering and analysis software

http://churchlab.github.io/millstone/

MIT License

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issues

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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 6 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 7 years ago
0
Velvetg runs out of memory during graph building

#687 glebkuznetsov opened 7 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