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
#3748 - Question about genome data installation because of invalid download link of mirbase
Issue -
State: open - Opened by lovebaboon1989 about 2 months ago
- 2 comments
#3747 - Installation fails with Mamba error: Nothing provides libsodium >=0.4,<1.0 needed by bcbio-nextgen-1.0.0-py27_0
Issue -
State: open - Opened by tpham2654 about 2 months ago
- 3 comments
#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
#3743 - File "abundance.h5" missing from salmon sample directory
Issue -
State: closed - Opened by fardellas 4 months ago
#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
#3729 - Error upgrading bcbio-nextgen to add the genome and an aligner
Issue -
State: open - Opened by moutazhelal 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
#3713 - On torque cluster, piped_bamprep "result not ready, cannot allocate memory" error
Issue -
State: open - Opened by fouriejoubert over 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
#3709 - Only header but no mutations were present in varscan vcf output.
Issue -
State: open - Opened by EvaPang2022 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
#3705 - Wrong bcbio-nextgen versioned pinned in requirements file for v1.2.2 and later
Issue -
State: open - Opened by asee-imagia over 1 year ago
- 1 comment
#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
#3690 - [main_samview] fail to read the header from "filename.sam".
Issue -
State: open - Opened by gabyrudd22 almost 2 years ago
#3689 - Error with bcbio_setup_genome.py: AttributeError: 'Namespace' object has no attribute 'cloudbiolinux'
Issue -
State: closed - Opened by amizeranschi almost 2 years ago
#3688 - Bringing back Docker support, possibly as a replacement for the various Conda environments
Issue -
State: open - Opened by amizeranschi almost 2 years ago
#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
#3676 - curl: (60) SSL certificate problem when downloading bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz
Issue -
State: closed - Opened by eylenth about 2 years ago
- 3 comments
#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
#3668 - setting -ploidy in yaml crashes gatk because existing default causes error: "Argument 'ploidy/sample-ploidy' cannot be specified more than once."
Issue -
State: closed - Opened by mjsduncan about 2 years ago
- 2 comments
#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
#3652 - ggd-run.sh error when installing sacCer3 genome data: "can't open file '/bin/python': [Errno 2] No such file or directory"
Issue -
State: closed - Opened by amizeranschi over 2 years ago
- 9 comments
#3651 - Unable to install bcbio (bcbio_nextgen.py not found)
Issue -
State: closed - Opened by gis-nlsim over 2 years ago
- 3 comments
#3650 - Error running bamsormadup (version 2.0.183): libmaus2.so.2: undefined symbol: _ZTIN6snappy4SinkE
Issue -
State: open - Opened by amizeranschi over 2 years ago
- 5 comments