From 90d219da6896bb040c5c0762aa570f50be454be9 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sun, 9 Apr 2023 17:32:01 -0400 Subject: [PATCH] rm more cluster_specific --- workflows/colocalization/Snakefile | 3 --- workflows/external/Snakefile | 4 ---- workflows/figures/Snakefile | 4 ---- workflows/references/Snakefile | 4 ---- 4 files changed, 15 deletions(-) diff --git a/workflows/colocalization/Snakefile b/workflows/colocalization/Snakefile index 700092cb7..ac0b0413f 100644 --- 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 index 53e2fc61e..9f8308c9d 100644 --- 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 index b236f36fb..e457a075d 100644 --- 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 index b1f8836d1..09bf49245 100644 --- 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)