bcbio/bcbio-nextgen issues and pull requests

#3649 - Installation issue conda error

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

#3648 - Cellranger mkref

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

#3647 - Samtools problem in python2 env, breaking Lumpy SV calling

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

#3646 - Optitype Error: SolverFactory was unable to create the solve "cbc"

Issue - State: open - Opened by gis-nlsim over 2 years ago

#3645 - bcbio installation remains at 1.2.8 after upgrade

Issue - State: closed - Opened by gis-nlsim over 2 years ago - 1 comment

#3644 - Feature request: pinned dependency versions for a specific bcbio release, to avoid future problems with faulty conda environment solving

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

#3643 - Does bcbio allow min_allele_frequency < 1 ?

Issue - State: closed - Opened by hanaecarrie over 2 years ago - 1 comment

#3642 - Is StringTie v2.2.0 with CRAM support in the latest bcbio release of dev version

Issue - State: open - Opened by WimSpee over 2 years ago - 3 comments

#3641 - Update GRCh37-dbnsfp.conf

Pull Request - State: closed - Opened by matthdsm over 2 years ago - 2 comments

#3640 - Update hg38-dbnsfp.conf

Pull Request - State: closed - Opened by matthdsm over 2 years ago - 2 comments

#3639 - bgzip error

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

#3638 - 404 Error during bcbio installation of human genome.

Issue - State: closed - Opened by gis-nlsim over 2 years ago - 5 comments

#3637 - Install Genomes Error

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

#3636 - Error in bcbio installation

Issue - State: open - Opened by keenhl over 2 years ago - 7 comments

#3635 - /usr/bin/env: 'python2' error for Manta

Issue - State: open - Opened by prasundutta87 over 2 years ago - 3 comments

#3634 - What is the option command of bowtie2 in the ATAC seq alignment?

Issue - State: closed - Opened by panic0918 over 2 years ago - 2 comments

#3633 - Smoove Lumpy error in structural variation pipeline

Issue - State: open - Opened by prasundutta87 over 2 years ago - 3 comments

#3632 - bcftools symbol lookup error (after bcbio v1.2.9 installation)

Issue - State: closed - Opened by prasundutta87 over 2 years ago - 9 comments

#3631 - GATK AnnotatedInervalCodec Exception (GATK4)

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

#3630 - STAR index error upon installation

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

#3629 - Issue while installing the latest version of bcbio (v1.2.9)

Issue - State: open - Opened by prasundutta87 over 2 years ago - 5 comments

#3626 - RNA-Seq salmon error

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

#3625 - Symlinks for samtools are not created for a fresh installation

Issue - State: closed - Opened by gabeng over 2 years ago - 1 comment

#3624 - Cannot install version 1.2.9 (fails at installing deepvariant trying to link non-existent google cloud account)

Issue - State: closed - Opened by tpham2654 over 2 years ago - 8 comments

#3612 - T2T CHM13 human reference genome

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

#3603 - bcbio_nextgen data upgrades when trying to download snpEff_v4_3_GRCh38.99.zip

Issue - State: closed - Opened by pvanheus over 2 years ago - 1 comment

#3599 - ggd-run.sh returned non-zero exit status 255

Issue - State: closed - Opened by gis-nlsim almost 3 years ago - 5 comments

#3597 - RNASeq STAR index building taking a long time

Issue - State: closed - Opened by gis-nlsim almost 3 years ago - 1 comment

#3565 - Error running bcbioRNASeq from within bcbio: there is no package called ‘bcbioRNASeq’

Issue - State: open - Opened by amizeranschi almost 3 years ago - 73 comments

#3557 - Samtools error when installing bcbio genome data in bcbio: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Issue - State: open - Opened by amizeranschi almost 3 years ago - 22 comments

#3554 - Running sample configuration file is giving error

Issue - State: closed - Opened by aswani1208 almost 3 years ago - 5 comments

#3545 - errors with atacseq

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

#3539 - Mutect2 and PureCN: also genotype sites present in the PoN

Pull Request - State: closed - Opened by lbeltrame almost 3 years ago - 6 comments

#3530 - sample set up for gatk-haplotype-joint

Issue - State: open - Opened by DiyaVaka about 3 years ago - 6 comments
Labels: question

#3447 - MACS error in ATAC-Seq pipeline

Issue - State: closed - Opened by sbdaxia over 3 years ago - 10 comments

#3387 - Issue with mutect PON causing symbolic link error

Issue - State: open - Opened by waemm almost 4 years ago - 8 comments

#3318 - installation issues

Issue - State: closed - Opened by DiyaVaka about 4 years ago - 19 comments

#3179 - Salmon version update

Issue - State: closed - Opened by sd282 over 4 years ago - 2 comments

#3124 - mosdepth index files missing?

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

#2969 - Installation problems with system-wide conda

Issue - State: closed - Opened by karl616 almost 5 years ago - 9 comments

#2937 - Add support for germline resources (from gnomAD) in Mutect2

Pull Request - State: closed - Opened by lbeltrame about 5 years ago - 4 comments

#2932 - COSMIC (v90) support

Issue - State: closed - Opened by jxshi about 5 years ago - 12 comments
Labels: enhancement

#2923 - [404 error] Running GGD recipe: hg38 varpon 20181105

Issue - State: closed - Opened by LimWChing about 5 years ago - 11 comments
Labels: bug

GitHub / bcbio/bcbio-nextgen issues and pull requests