Ecosyste.ms: Issues

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GitHub / bcbio/bcbio-nextgen issues and pull requests

#3749 - Discontinuation of bcbio-nextgen project

Issue - State: open - Opened by lpantano about 2 months ago - 1 comment

#3746 - Update ci.yml

Pull Request - State: closed - Opened by lpantano 3 months ago

#3745 - Create ci.yml

Pull Request - State: closed - Opened by lpantano 3 months ago

#3744 - Installation fails

Issue - State: open - Opened by PCanavelli 3 months ago - 3 comments

#3742 - Hisat 2 error

Issue - State: open - Opened by Maria6642 5 months ago - 1 comment

#3741 - remove Python2 crumbs

Pull Request - State: open - Opened by a-detiste 5 months ago - 4 comments

#3740 - KeyError: 'MB1' ' returned non-zero exit status 1. when running scRNA-seq analysis for indropv3

Issue - State: open - Opened by juychen 8 months ago - 1 comment
Labels: known-issue-and-how-to-fix

#3739 - MultiQC error: cannot import name 'TypedDict' from 'typing'

Issue - State: open - Opened by VerenaPass 8 months ago - 2 comments

#3738 - add recommonmark module to readthedocs conf

Pull Request - State: closed - Opened by naumenko-sa 9 months ago

#3737 - return submodules to readthedocs config

Pull Request - State: closed - Opened by naumenko-sa 9 months ago

#3736 - add os and python to readthedocs yml

Pull Request - State: closed - Opened by naumenko-sa 9 months ago

#3735 - exclude submodules in readthedocs build

Pull Request - State: closed - Opened by naumenko-sa 9 months ago

#3734 - Save meetas work

Pull Request - State: closed - Opened by naumenko-sa 9 months ago

#3733 - deprecate SC user story

Pull Request - State: closed - Opened by naumenko-sa 9 months ago

#3732 - updating atac user story documentation

Pull Request - State: closed - Opened by mistrm82 10 months ago

#3731 - ATAC-seq pipeline: what exampley is ready.bam?

Issue - State: closed - Opened by naumenko-sa 10 months ago - 1 comment

#3730 - ATAC-seq

Issue - State: open - Opened by naumenko-sa 10 months ago

#3728 - vcfanno bug

Issue - State: open - Opened by wangpenhok 11 months ago

#3727 - resources assignment when perform parallel jobs

Issue - State: open - Opened by wangpenhok 11 months ago - 1 comment

#3726 - Anaconda channels

Issue - State: closed - Opened by gis-nlsim 11 months ago - 1 comment

#3725 - miRBase old versions are no longer available

Issue - State: closed - Opened by rchekaluk 11 months ago

#3724 - Files are no longer available on miRBase ftp site

Issue - State: closed - Opened by rchekaluk 11 months ago

#3723 - miRBase download files are not compressed

Issue - State: closed - Opened by rchekaluk 11 months ago

#3722 - miRBase genomes URLs have changed

Issue - State: closed - Opened by rchekaluk 11 months ago

#3721 - miRBase certificate error

Issue - State: closed - Opened by rchekaluk 11 months ago

#3720 - mm10 Genome Installation Error

Issue - State: open - Opened by daisysdan 11 months ago

#3719 - bcbio run not running samples in parallel

Issue - State: closed - Opened by toddcreasy 11 months ago - 2 comments

#3718 - Can bcbio customize the user-defined GLIBC directory?

Issue - State: open - Opened by lovebaboon1989 12 months ago - 7 comments

#3717 - Does bcbio support smooth restart when a job is stopped?

Issue - State: closed - Opened by lovebaboon1989 12 months ago - 2 comments

#3716 - Error during alignment using STAR

Issue - State: closed - Opened by tdelisper 12 months ago - 2 comments

#3715 - umi stat

Issue - State: open - Opened by dauss75 about 1 year ago - 1 comment

#3714 - Failed in generating genome files

Issue - State: closed - Opened by gis-nlsim about 1 year ago - 1 comment

#3712 - Installing bcbio in macos in VM fails

Issue - State: closed - Opened by GACGAMA over 1 year ago - 1 comment

#3711 - Docker version of Bcbio

Issue - State: open - Opened by Adrian-Zet over 1 year ago

#3710 - Fail to build Normal DB in PureCN pipeline

Issue - State: open - Opened by WuRAFY over 1 year ago

#3708 - IBM Power9 (ppc64le) support

Issue - State: closed - Opened by um-pdavila over 1 year ago - 1 comment

#3707 - Error installing hg38 dbsnp data: ERROR 404: Not Found

Issue - State: open - Opened by amizeranschi over 1 year ago - 3 comments

#3706 - tabix error on effects-ploidyfix.vcf.gz

Issue - State: open - Opened by hongenxu over 1 year ago

#3704 - Question on parrallelization with callable regions

Issue - State: closed - Opened by nvnieuwk over 1 year ago - 2 comments

#3703 - Update BDGP6-resources.yaml

Pull Request - State: closed - Opened by naumenko-sa over 1 year ago

#3702 - Java error after fresh install of v1.2.9

Issue - State: open - Opened by lindakohn over 1 year ago - 5 comments

#3701 - Question: callable regions generation

Issue - State: closed - Opened by matthdsm over 1 year ago - 2 comments

#3700 - Methylation pipeline

Issue - State: open - Opened by Adrian-Zet over 1 year ago - 2 comments

#3699 - Error during install - dbsnp issue

Issue - State: open - Opened by jchien-ucd over 1 year ago - 15 comments

#3698 - COSMIC NEWER VERSION SUPPORT(v94 and later)

Issue - State: open - Opened by wangpenhok over 1 year ago - 6 comments

#3697 - subset of chromosome regions bed file

Issue - State: closed - Opened by TSL-RamKrishna over 1 year ago - 1 comment

#3696 - Unable to install on M1 mac

Issue - State: closed - Opened by alasfar-lina over 1 year ago - 1 comment

#3695 - Provide a bait file to Picard's CollectHsMetrics

Pull Request - State: open - Opened by asee-imagia over 1 year ago

#3694 - Empty tmpcbl/ref-transcripts.gtf created while building mm39 genome

Issue - State: closed - Opened by daisysdan over 1 year ago - 2 comments

#3693 - ValueError: Could not find directory in config for snpeff

Issue - State: open - Opened by azzatha over 1 year ago - 1 comment

#3692 - recalibrate=true fails, Unsupported class file major version 55

Issue - State: open - Opened by asalimih almost 2 years ago - 3 comments

#3691 - Add --cloudbiolinux argument

Pull Request - State: closed - Opened by amizeranschi almost 2 years ago - 2 comments

#3687 - installing from scratch using ether conda or mamba fails on perl version?

Issue - State: open - Opened by LeoWelter almost 2 years ago - 6 comments

#3686 - Installing from scratch is failing due to Conda

Issue - State: closed - Opened by amizeranschi almost 2 years ago - 1 comment

#3685 - Using bcbio-nextgen in two nodes " pbs torque"

Issue - State: closed - Opened by Talo07 almost 2 years ago - 1 comment

#3684 - fix srnaseq bug

Pull Request - State: closed - Opened by naumenko-sa almost 2 years ago

#3683 - Questions : use of joint calling with octopus and gnomad genome

Issue - State: open - Opened by Titos789 almost 2 years ago - 1 comment

#3682 - Processing data with unknown capture panel

Issue - State: open - Opened by waemm almost 2 years ago - 1 comment

#3681 - Added tool

Issue - State: open - Opened by Talo07 almost 2 years ago - 3 comments

#3680 - CVE-2007-4559 Patch

Pull Request - State: open - Opened by TrellixVulnTeam almost 2 years ago

#3679 - bcbio 1.2.9 installation error in the HPC cluster

Issue - State: closed - Opened by kimal999 almost 2 years ago - 3 comments

#3678 - New installation error with current (21 Oct 2022) installer

Issue - State: open - Opened by fouriejoubert almost 2 years ago - 2 comments

#3677 - Issue in GATK base Recalibration step while aligning tumor WGS sample

Issue - State: open - Opened by AkankshaFarswan almost 2 years ago - 1 comment

#3675 - subprocess.CalledProcessError: Command '[ ]' returned non-zero exit status 1

Issue - State: open - Opened by KTison about 2 years ago - 3 comments

#3674 - R package version error when combining tx2gene CSV files

Issue - State: open - Opened by dnbuckley about 2 years ago - 14 comments

#3673 - Split up broad and narrow antibodies

Pull Request - State: closed - Opened by Gammerdinger about 2 years ago - 1 comment

#3672 - Question: set walltime for ipython jobs

Issue - State: closed - Opened by matthdsm about 2 years ago - 2 comments

#3671 - issue with STAR alignment crashes salmon

Issue - State: open - Opened by mjsduncan about 2 years ago - 3 comments

#3670 - genome download link error

Issue - State: open - Opened by jenny8030 about 2 years ago

#3669 - documentation request: pool-seq user story

Issue - State: open - Opened by mjsduncan about 2 years ago - 1 comment

#3667 - docs: Fix a few typos

Pull Request - State: closed - Opened by timgates42 about 2 years ago - 1 comment

#3666 - Bump pinned mamba version

Pull Request - State: closed - Opened by rchekaluk about 2 years ago - 1 comment

#3665 - Is STAR-fusion currently available in the pipeline?

Issue - State: closed - Opened by EvaPang2022 about 2 years ago - 2 comments

#3664 - snpEff database download url for BDGP6 genome has changed

Issue - State: open - Opened by mjsduncan about 2 years ago - 5 comments

#3663 - Building custom genome CHM13

Issue - State: open - Opened by Hmllycat about 2 years ago

#3662 - fgbio and manta incompatibilities with duplex UMIs

Issue - State: open - Opened by kmendler over 2 years ago - 1 comment

#3661 - Installing 1.2.9 error

Issue - State: open - Opened by pengxiao78 over 2 years ago - 10 comments

#3660 - How to get the runtime of each caller when I use multiple caller in yaml file?

Issue - State: closed - Opened by LeiHaoa over 2 years ago - 2 comments
Labels: question

#3659 - PBSPro's qsub on our cluster needs #PBS -P project_id

Issue - State: open - Opened by fouriejoubert over 2 years ago - 2 comments

#3658 - snpEff v4.3GRCh38.99.zip unavailable

Issue - State: open - Opened by IBEXCluster over 2 years ago - 5 comments

#3657 - Mapping efficiency very low (88 % of reads too short)

Issue - State: closed - Opened by jcostea over 2 years ago

#3656 - Stripping underscores from otherwise numeric identifiers

Issue - State: closed - Opened by ameynert over 2 years ago - 4 comments

#3655 - Somatic tumor only variant calling pipeline with UMIs step by step

Issue - State: closed - Opened by kokyriakidis over 2 years ago - 6 comments

#3654 - failed in downloading gnomad sites

Issue - State: open - Opened by lmanchon over 2 years ago - 3 comments
Labels: bug

#3653 - State of the project

Issue - State: open - Opened by lbeltrame over 2 years ago - 8 comments

#3651 - Unable to install bcbio (bcbio_nextgen.py not found)

Issue - State: closed - Opened by gis-nlsim over 2 years ago - 3 comments