Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Pipe 48 fix broken conda dependency #267

Merged
merged 2 commits into from
Feb 28, 2022
Merged

Pipe 48 fix broken conda dependency #267

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
c6f5a21
bump ver
leepc12 Feb 24, 2022
7a692c7
fix conda ncurses issue
leepc12 Feb 24, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions chip.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ struct RuntimeEnvironment {
}

workflow chip {
String pipeline_ver = 'v2.1.4'
String pipeline_ver = 'v2.1.5'

meta {
version: 'v2.1.4'
version: 'v2.1.5'

author: 'Jin wook Lee'
email: '[email protected]'
Expand All @@ -19,8 +19,8 @@ workflow chip {

specification_document: 'https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit?usp=sharing'

default_docker: 'encodedcc/chip-seq-pipeline:v2.1.4'
default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
default_docker: 'encodedcc/chip-seq-pipeline:v2.1.5'
default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.5.sif'
croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v5.json'

parameter_group: {
Expand Down Expand Up @@ -71,8 +71,8 @@ workflow chip {
}
input {
# group: runtime_environment
String docker = 'encodedcc/chip-seq-pipeline:v2.1.4'
String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
String docker = 'encodedcc/chip-seq-pipeline:v2.1.5'
String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.5.sif'
String conda = 'encode-chip-seq-pipeline'
String conda_macs2 = 'encode-chip-seq-pipeline-macs2'
String conda_spp = 'encode-chip-seq-pipeline-spp'
Expand Down
9 changes: 6 additions & 3 deletions scripts/install_conda_env.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,12 @@ conda create -n encode-chip-seq-pipeline-macs2 --file ${SH_SCRIPT_DIR}/requireme
conda create -n encode-chip-seq-pipeline-spp --file ${SH_SCRIPT_DIR}/requirements.spp.txt \
--override-channels -c r -c bioconda -c defaults -y

# adhoc fix for https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/259
# force-install readline 6.2 from conda-forge (ignoring dependencies)
conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y readline==6.2 -c conda-forge
# adhoc fix for the following issues:
# - https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/259
# - https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/265
# force-install readline 6.2, ncurses 5.9 from conda-forge (ignoring dependencies)
conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y \
readline==6.2 ncurses==5.9 -c conda-forge

echo "$(date): Done successfully."

Expand Down