From db6c45b633ad77a3031dae6b9b65d414ccf94ea3 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <sascha.meiers.embl@gmail.com>
Date: Fri, 30 Nov 2018 10:44:34 +0100
Subject: [PATCH] Fixing a Singularity issue with PYTHONPATH (see
https://bitbucket.org/snakemake/snakemake/issues/1031)
---
Snakefile | 46 ++++++++++++++++++++++++++++++++++++++++------
1 file changed, 40 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index 27d3bda..ba80dbe 100644
--- a/Snakefile
+++ b/Snakefile
@@ -230,6 +230,7 @@ rule estimate_ploidy:
"log/estimate_ploidy/{sample}/{chrom}.log"
shell:
"""
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
python utils/ploidy-estimator.py --chromosome {wildcards.chrom} {input} > {output} 2> {log}
"""
@@ -327,7 +328,10 @@ rule generate_halo_json:
log:
"log/generate_halo_json/{sample}/{windows}.{windows}.log"
shell:
- "(./utils/counts_to_json.py {input.counts} | gzip > {output.json}) 2> {log}"
+ """
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
+ (./utils/counts_to_json.py {input.counts} | gzip > {output.json}) 2> {log}
+ """
@@ -452,7 +456,8 @@ rule merge_blacklist_bins:
"log/merge_blacklist_bins/{window}.log"
shell:
"""
- utils/merge-blacklist.py --merge_distance 500000 {input.norm} --whitelist {input.whitelist} --min_whitelist_interval_size 100000 > {output.merged} 2> {log}
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
+ utils/merge-blacklist.py --merge_distance 500000 {input.norm} --whitelist {input.whitelist} --min_whitelist_interval_size 100000 > {output.merged} 2>> {log}
"""
rule normalize_counts:
@@ -572,7 +577,23 @@ rule segmentation_selection:
cellnames = lambda wc: ",".join(cell for cell in CELL_PER_SAMPLE[wc.sample]),
sce_min_distance = 500000,
shell:
- "./utils/detect_strand_states.py --sce_min_distance {params.sce_min_distance} --sce_add_cutoff {wildcards.additional_sce_cutoff}000000 --min_diff_jointseg {wildcards.min_diff_jointseg} --min_diff_singleseg {wildcards.min_diff_singleseg} --output_jointseg {output.jointseg} --output_singleseg {output.singleseg} --output_strand_states {output.strand_states} --samplename {wildcards.sample} --cellnames {params.cellnames} {input.info} {input.counts} {input.jointseg} {input.singleseg} > {log} 2>&1"
+ """
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
+ ./utils/detect_strand_states.py \
+ --sce_min_distance {params.sce_min_distance} \
+ --sce_add_cutoff {wildcards.additional_sce_cutoff}000000 \
+ --min_diff_jointseg {wildcards.min_diff_jointseg} \
+ --min_diff_singleseg {wildcards.min_diff_singleseg} \
+ --output_jointseg {output.jointseg} \
+ --output_singleseg {output.singleseg} \
+ --output_strand_states {output.strand_states} \
+ --samplename {wildcards.sample} \
+ --cellnames {params.cellnames} \
+ {input.info} \
+ {input.counts} \
+ {input.jointseg} \
+ {input.singleseg} > {log} 2>&1
+ """
################################################################################
@@ -619,7 +640,11 @@ rule filter_calls:
output:
calls = "sv_calls/{sample}/{window}_fixed_norm.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+_scedist[0-9\\.]+}/simpleCalls_llr{llr}_poppriors{pop_priors,(TRUE|FALSE)}_haplotags{use_haplotags,(TRUE|FALSE)}_gtcutoff{gtcutoff,[0-9\\.]+}_regfactor{regfactor,[0-9]+}_filterTRUE.txt"
shell:
- 'utils/apply_filter.py {input.inputcalls} {input.mergedcalls} > {output.calls}'
+ """
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
+ utils/apply_filter.py {input.inputcalls} {input.mergedcalls} > {output.calls}
+ """
+
rule mosaiClassifier_calc_probs:
@@ -653,7 +678,13 @@ rule call_complex_regions:
log:
"log/call_complex_regions/{sample}/{windows}.{bpdens}.{method}.log"
shell:
- "utils/call-complex-regions.py --merge_distance 5000000 --ignore_haplotypes --min_cell_count 2 {input.calls} > {output.complex} 2>{log}"
+ """
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
+ utils/call-complex-regions.py \
+ --merge_distance 5000000 \
+ --ignore_haplotypes \
+ --min_cell_count 2 {input.calls} > {output.complex} 2>{log}
+ """
rule postprocessing_filter:
@@ -679,7 +710,10 @@ rule postprocessing_sv_group_table:
output:
grouptrack = "postprocessing/group-table/{sample}/{window}_fixed_norm.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+_scedist[0-9\\.]+}/simpleCalls_llr{llr}_poppriors{pop_priors,(TRUE|FALSE)}_haplotags{use_haplotags,(TRUE|FALSE)}_gtcutoff{gtcutoff,[0-9\\.]+}_regfactor{regfactor,[0-9]+}.tsv"
shell:
- 'utils/create-sv-group-track.py {input.calls} > {output.grouptrack}'
+ """
+ PYTHONPATH="" # Issue #1031 (https://bitbucket.org/snakemake/snakemake/issues/1031)
+ utils/create-sv-group-track.py {input.calls} > {output.grouptrack}
+ """
################################################################################
--
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