rm more cluster_specific

lcdb · Apr 9, 2023 · 90d219d · 90d219d
1 parent 4cac58a
commit 90d219d
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diff --git a/workflows/colocalization/Snakefile b/workflows/colocalization/Snakefile
@@ -8,7 +8,6 @@ import pandas as pd
 from lib import helpers, aligners
 from lib import utils
 from lib import common
-from lib import cluster_specific
 from lib.patterns_targets import RNASeqConfig, ChIPSeqConfig
 import os
 from snakemake.utils import makedirs
@@ -17,8 +16,6 @@ import yaml
 import numpy as np
 
 configfile: 'config/config.yaml'
-shell.prefix('set -euo pipefail; export TMPDIR={};'.format(cluster_specific.tempdir_for_biowulf()))
-shell.executable('/bin/bash')
 
 chipseq_config = ChIPSeqConfig('config/config.yaml', 'config/chipseq_patterns.yaml', workdir='../chipseq')
 

diff --git a/workflows/external/Snakefile b/workflows/external/Snakefile
@@ -1,13 +1,9 @@
 import sys
 sys.path.insert(0, srcdir('../..'))
-from lib import cluster_specific
 from lib import common
 import pybedtools
 
 
-shell.prefix('set -euo pipefail; export TMPDIR={};'.format(cluster_specific.tempdir_for_biowulf()))
-shell.executable('/bin/bash')
-
 # This is a useful construct for mapping intended output filenames to the URLs
 # they come from
 modencode = {

diff --git a/workflows/figures/Snakefile b/workflows/figures/Snakefile
@@ -23,12 +23,8 @@ sys.path.insert(0, srcdir('../..'))
 import os
 from lib import utils
 from lib import common
-from lib import cluster_specific
 from lib.patterns_targets import RNASeqConfig, ChIPSeqConfig
 
-shell.prefix('set -euo pipefail; export TMPDIR={};'.format(cluster_specific.tempdir_for_biowulf()))
-shell.executable('/bin/bash')
-
 rnaseq_config = RNASeqConfig('config/config.yaml', 'config/rnaseq_patterns.yaml', workdir='../rnaseq')
 chipseq_config = ChIPSeqConfig('config/config.yaml', 'config/chipseq_patterns.yaml', workdir='../chipseq')
 

diff --git a/workflows/references/Snakefile b/workflows/references/Snakefile
@@ -20,10 +20,6 @@ from lib import common
 
 config = common.load_config(config)
 
-tempfile.tempdir = cluster_specific.tempdir_for_biowulf()
-
-shell.prefix('set -euo pipefail; export TMPDIR={};'.format(cluster_specific.tempdir_for_biowulf()))
-shell.executable('/bin/bash')
 references_dir = common.get_references_dir(config)
 refdict, conversion_kwargs = common.references_dict(config)