bcbio bcbio-nextgen-vm issues

bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines

MIT License

65 stars 17 forks source link

issues

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docker image ModuleNotFoundError

#192 ltnetcase opened 3 years ago
1
minimap2 support

#191 fgvieira opened 4 years ago
0
Delete txtmp directory automatically after successful genome installation

#190 hackdna opened 4 years ago
0
Error while downloading docker image and tools - non-zero exit status 1

#189 sarthi2395 opened 4 years ago
0
Add Docker and CWL tests

#188 hackdna closed 4 years ago
1
test_cwl_arvados_workflow fails due to HttpError

#187 hackdna opened 4 years ago
0
test_cwl_docker_joint_calling_workflow fails due to TypeError

#186 hackdna opened 4 years ago
0
test_docker_ipython does not run to completion

#185 hackdna opened 4 years ago
0
Add support for macOS installation using Vagrant

#184 hackdna closed 4 years ago
1
Update stale URLs in README.md

#183 hackdna closed 4 years ago
0
Convert README.rst to README.md

#182 hackdna closed 4 years ago
1
Add TravisCI tests

#181 hackdna closed 4 years ago
1
boto ec2.import_key_pair expects bytes, not a str

#180 cariaso closed 4 years ago
1
Kraken not availble inside the docker image

#179 cvaske opened 4 years ago
2
Version return is missing

#178 mjsteinbaugh opened 5 years ago
0
Quay registry deprecation notice on clean install

#177 mjsteinbaugh opened 5 years ago
0
Tag support for install call

#176 mjsteinbaugh closed 5 years ago
3
Toil, cwl, bcbio - ImportError: cannot import name 'fillInDefaults' from 'cwltool.process'

#175 dennis-kao closed 5 years ago
2
CalledProcessError: Command '['bash', '/mnt/biodata/genomes/Hsapiens/GRCh37/txtmp/ggd-run.sh']' returned non-zero exit status 1

#174 iJasonZHOU closed 5 years ago
6
bioconda recipe, remove cromwell pin

#173 matthdsm closed 5 years ago
2
remote data on S3

#172 matthdsm opened 5 years ago
1
gatk-framework: command not found

#171 romanzac opened 5 years ago
2
Where to find sample_config.yaml

#170 romanzac closed 5 years ago
3
GRCh37 default build for bcbio: does it include decoys?

#169 RobertWBaldwin opened 6 years ago
3
ImportError: No module named callbacks

#168 PatrickJReed closed 6 years ago
2
Unable to setup AWS

#167 gnvalbuena closed 6 years ago
4
GATK4

#166 willmclaren closed 6 years ago
3
elasticloud not installed?

#165 willmclaren closed 6 years ago
3
Change system_find_projects permission to "VIEW"

#164 yihchii closed 6 years ago
1
bcbio_vm.py aws cluster start give 'ansible_utils' is not defined

#163 apastore opened 7 years ago
5
Typo in bcbiovm/aws/common.py prevents starting a cluster

#162 DavidQuigley closed 7 years ago
1
problem after update

#161 silvanopiazza closed 7 years ago
1
Unable to setup new cluster

#160 kyubivela opened 7 years ago
1
slurm bcbio_submit.sh job pending

#159 tomsing1 opened 7 years ago
3
ipython error when trying to submit jobs on AWS cluster: ERROR | Controller start failed

#158 tomsing1 closed 7 years ago
10
Reopening issue about VPC creation in the wrong zone

#157 tomsing1 closed 7 years ago
2
IAM user bcbio is created with full_admin_access

#156 gabeng closed 8 years ago
2
VPC always created in us-east-1

#155 gabeng closed 8 years ago
1
support for Openstack

#154 gmihaiescu opened 8 years ago
1
--no-check-certificate error

#153 firatuyulur closed 8 years ago
2
latest available lustre-utils not downloading

#152 gnvalbuena opened 8 years ago
8
valueerror samtools GRCh37

#151 firatuyulur opened 8 years ago
5
Ensemble stage process failed

#150 mortunco closed 8 years ago
8
Using bcbio_setup_genome.py with bcbio-nextgen-vm?

#149 tomsing1 closed 8 years ago
3
bam_clean error: Bad Input

#148 mortunco closed 8 years ago
3
Bcbio Stopping vm Cluster I want to keep the cluster.

#147 mortunco closed 8 years ago
1
Indel Calling Scalpel-Pindel No

#146 mortunco closed 8 years ago
4
bcbio-vm stucks at a step during run without any errors?

#145 mortunco closed 8 years ago
15
bcbio-vm running on cluster + setting cluster+ template issues

#144 mortunco closed 8 years ago
4
Amazon S3 bcbio_vm.py aws vpc error

#143 mortunco closed 8 years ago
3