diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 2c0f1c31a9c46b5f9f45699f3c1eb506d6c62e10..07407ef8c8d5c3b4f34f0ade0b9ff2c8d78b69ce 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -41,7 +41,7 @@ process {
executor = 'local'
}
withName: callPeaksMACS {
- module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'phantompeakqualtools/1.2', 'UCSC_userApps/v317', 'bedtools/2.26.0']
+ module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'UCSC_userApps/v317', 'bedtools/2.26.0']
queue = '128GB,256GB,256GBv1'
}
withName: consensusPeaks {
diff --git a/workflow/main.nf b/workflow/main.nf
index a8c50272131ced87f134cf63241032ceddda2f98..ddeb067dc952c3d85d499fd1dcd81e7df0f3f774 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -99,7 +99,8 @@ process trimReads {
output:
set sampleId, file('*.fq.gz'), experimentId, biosample, factor, treatment, replicate, controlId into trimmedReads
- file('*trimming_report.txt') into trimgalore_results
+ file('*trimming_report.txt') into trimgaloreResults
+ file('version_*.txt') into trimReadsVersions
script:
@@ -131,6 +132,7 @@ process alignReads {
set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into mappedReads
file '*.flagstat.qc' into mappedReadsStats
+ file('version_*.txt') into alignReadsVersions
script:
@@ -164,6 +166,7 @@ process filterReads {
file '*.flagstat.qc' into dedupReadsStats
file '*.pbc.qc' into dedupReadsComplexity
file '*.dedup.qc' into dupReads
+ file('version_*.txt') into filterReadsVersions
script:
@@ -198,7 +201,8 @@ process experimentQC {
output:
- file '*.{pdf,npz}' into deepToolsStats
+ file '*.{pdf,npz}' into experimentQCStats
+ file('version_*.txt') into experimentQCVersions
script:
@@ -221,6 +225,7 @@ process convertReads {
output:
set sampleId, file('*.tagAlign.gz'), file('*.bed{pe,se}.gz'), experimentId, biosample, factor, treatment, replicate, controlId into tagReads
+ file('version_*.txt') into convertReadsVersions
script:
@@ -250,7 +255,8 @@ process crossReads {
output:
set sampleId, seTagAlign, tagAlign, file('*.cc.qc'), experimentId, biosample, factor, treatment, replicate, controlId into xcorReads
- set file('*.cc.qc'), file('*.cc.plot.pdf') into xcorReadsStats
+ set file('*.cc.qc'), file('*.cc.plot.pdf') into crossReadsStats
+ file('version_*.txt') into crossReadsVersions
script:
@@ -342,7 +348,8 @@ process callPeaksMACS {
output:
set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks
- file '*.xls' into summit
+ file '*.xls' into callPeaksMACSsummit
+ file('version_*.txt') into callPeaksMACSVersions
script:
@@ -383,6 +390,7 @@ process consensusPeaks {
file 'design_diffPeaks.csv' into designDiffPeaks
file 'design_annotatePeaks.tsv' into designAnnotatePeaks, designMotifSearch
file 'unique_experiments.csv' into uniqueExperiments
+ file('version_*.txt') into consensusPeaksVersions
script:
@@ -404,6 +412,7 @@ process peakAnnotation {
output:
file "*chipseeker*" into peakAnnotation
+ file('version_*.txt') into peakAnnotationVersions
script:
@@ -413,7 +422,7 @@ process peakAnnotation {
}
-// Motif Search Peaks
+// Motif Search Peaks
process motifSearch {
publishDir "$outDir/${task.process}", mode: 'copy'
@@ -426,6 +435,7 @@ process motifSearch {
file "*memechip" into motifSearch
file "*narrowPeak" into filteredPeaks
+ file('version_*.txt') into motifSearchVersions
script:
@@ -454,6 +464,7 @@ process diffPeaks {
file '*_diffbind.csv' into diffPeaksCounts
file '*.pdf' into diffPeaksStats
file 'normcount_peaksets.txt' into normCountPeaks
+ file('version_*.txt') into diffPeaksVersions
when:
noUniqueExperiments > 1
@@ -463,3 +474,29 @@ process diffPeaks {
Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
"""
}
+
+// Collect Software Versions
+process softwareVersions {
+
+ input:
+
+ trimReadsVersions
+ alignReadsVersions
+ filterReadsVersions
+ convertReadsVersions
+ crossReadsVersions
+ callPeaksMACSVersions
+ consensusPeaksVersions
+ peakAnnotationVersions
+ motifSearchVersions
+ diffPeaksVersions
+ experimentQCVersions
+
+ output:
+ file 'software_versions_mqc.yaml' into softwareVersions
+
+ script:
+ """
+ software_report.py > software_versions_mqc.yaml
+ """
+}
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 4bc8d79296150f64c1a1eed2ecba0b5e33b597d1..ff826b6a1f3af6bd8e38fa3555912ee7dda96609 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -35,6 +35,11 @@ if(genome_assembly=='GRCh37') {
annodb <- 'org.Hs.eg.db'
}
+# Output version of ChIPseeker
+chipseeker_version = packageVersion('ChIPseeker')
+write.table(paste("Version", chipseeker_version), file = "version_ChIPseeker.txt", sep = "\t",
+ row.names = FALSE, col.names = FALSE)
+
# Load design file
design <- read.csv(design_file, sep ='\t')
files <- as.list(as.character(design$Peaks))
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 17b1414b6236ee5cfda0d1c0694a988ecea237c9..38e03cc89d6c91d1d9f8247aa7396e2f9262cde6 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -5,6 +5,7 @@
import os
import argparse
import shutil
+import subprocess
import logging
import utils
from xcor import xcor as calculate_xcor
@@ -69,16 +70,19 @@ def check_tools():
logger.info('Checking for required libraries and components on this system')
- r_path = shutil.which("R")
- if r_path:
- logger.info('Found R: %s', r_path)
- else:
- logger.error('Missing R')
- raise Exception('Missing R')
-
macs_path = shutil.which("macs2")
if r_path:
logger.info('Found MACS2: %s', macs_path)
+
+ # Get Version
+ macs_version_command = "macs2 --version"
+ macs_version = subprocess.check_output(macs_version_command, shell=True, stderr=subprocess.STDOUT)
+
+ # Write to file
+ macs_file = open("version_macs.txt", "wb")
+ macs_file.write(macs_version)
+ macs_file.close()
+
else:
logger.error('Missing MACS2')
raise Exception('Missing MACS2')
@@ -86,6 +90,18 @@ def check_tools():
bg_bw_path = shutil.which("bedGraphToBigWig")
if bg_bw_path:
logger.info('Found bedGraphToBigWig: %s', bg_bw_path)
+
+ # Get Version
+ bg_bw_version_command = "bedGraphToBigWig"
+ try:
+ subprocess.check_output(bg_bw_version_command, shell=True, stderr=subprocess.STDOUT)
+ except subprocess.CalledProcessError as e:
+ bg_bw_version = e.output
+
+ # Write to file
+ bg_bw_file = open("version_bedGraphToBigWig.txt", "wb")
+ bg_bw_file.write(bg_bw_version)
+ bg_bw_file.close()
else:
logger.error('Missing bedGraphToBigWig')
raise Exception('Missing bedGraphToBigWig')
@@ -93,6 +109,16 @@ def check_tools():
bedtools_path = shutil.which("bedtools")
if bedtools_path:
logger.info('Found bedtools: %s', bedtools_path)
+
+ # Get Version
+ bedtools_version_command = "bedtools --version"
+ bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
+
+ # Write to file
+ bedtools_file = open("version_bedtools.txt", "wb")
+ bedtools_file.write(bedtools_version)
+ bedtools_file.close()
+
else:
logger.error('Missing bedtools')
raise Exception('Missing bedtools')
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index bba7c6f16e49b7ea608d50546ec0b5af21ed4448..43fe5cfee1ceccc13c563d14c8547c391dbd4542 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -54,6 +54,15 @@ def check_tools():
bedtools_path = shutil.which("bedtools")
if bedtools_path:
logger.info('Found bedtools: %s', bedtools_path)
+
+ # Get Version
+ bedtools_version_command = "bedtools --version"
+ bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
+
+ # Write to file
+ bedtools_file = open("version_bedtools.txt", "wb")
+ bedtools_file.write(bedtools_version)
+ bedtools_file.close()
else:
logger.error('Missing bedtools')
raise Exception('Missing bedtools')
@@ -61,6 +70,15 @@ def check_tools():
samtools_path = shutil.which("samtools")
if samtools_path:
logger.info('Found samtools: %s', samtools_path)
+
+ # Get Version
+ samtools_version_command = "samtools --version"
+ samtools_version = subprocess.check_output(samtools_version_command, shell=True)
+
+ # Write to file
+ samtools_file = open("version_samtools.txt", "wb")
+ samtools_file.write(samtools_version)
+ samtools_file.close()
else:
logger.error('Missing samtools')
raise Exception('Missing samtools')
diff --git a/workflow/scripts/diff_peaks.R b/workflow/scripts/diff_peaks.R
index aae1d24751f24396fff6fe712c28be27e36b0db3..68fda5624018ea6168a63242dc2e47ad7178a47d 100644
--- a/workflow/scripts/diff_peaks.R
+++ b/workflow/scripts/diff_peaks.R
@@ -11,6 +11,11 @@ if (length(args) != 1) {
stop("Usage: diff_peaks.R annotate_design.tsv ", call.=FALSE)
}
+# Output version of DiffBind
+diffibind_version = packageVersion('DiffBind')
+write.table(paste("Version", diffibind_version), file = "version_DiffBind.txt", sep = "\t",
+ row.names = FALSE, col.names = FALSE)
+
# Build DBA object from design file
data <- dba(sampleSheet=args[1])
data <- dba.count(data)
diff --git a/workflow/scripts/experiment_qc.py b/workflow/scripts/experiment_qc.py
index 466f84795f7c2783f68c166a8c53dcc268fd19ff..cf22338664a16157da2ad3b1c107a2af6d2372de 100644
--- a/workflow/scripts/experiment_qc.py
+++ b/workflow/scripts/experiment_qc.py
@@ -52,6 +52,15 @@ def check_tools():
deeptools_path = shutil.which("deeptools")
if deeptools_path:
logger.info('Found deeptools: %s', deeptools_path)
+
+ # Get Version
+ deeptools_version_command = "deeptools --version"
+ deeptools_version = subprocess.check_output(deeptools_version_command, shell=True, stderr=subprocess.STDOUT)
+
+ # Write to file
+ deeptools_file = open("version_deeptools.txt", "wb")
+ deeptools_file.write(deeptools_version)
+ deeptools_file.close()
else:
logger.error('Missing deeptools')
raise Exception('Missing deeptools')
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index 920e0090a3fe69d50dd014e8541b5b9916cabecb..ab63c423f613cef1fcdc2eaf91828b9b6d95b128 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -62,6 +62,15 @@ def check_tools():
samtools_path = shutil.which("samtools")
if samtools_path:
logger.info('Found samtools: %s', samtools_path)
+
+ # Get Version
+ samtools_version_command = "samtools --version"
+ samtools_version = subprocess.check_output(samtools_version_command, shell=True)
+
+ # Write to file
+ samtools_file = open("version_samtools.txt", "wb")
+ samtools_file.write(samtools_version)
+ samtools_file.close()
else:
logger.error('Missing samtools')
raise Exception('Missing samtools')
@@ -69,6 +78,18 @@ def check_tools():
sambamba_path = shutil.which("sambamba")
if sambamba_path:
logger.info('Found sambamba: %s', sambamba_path)
+
+ # Get Version
+ sambamba_version_command = "sambamba"
+ try:
+ subprocess.check_output(sambamba_version_command, shell=True, stderr=subprocess.STDOUT)
+ except subprocess.CalledProcessError as e:
+ sambamba_version = e.output
+
+ # Write to file
+ sambamba_file = open("version_sambamba.txt", "wb")
+ sambamba_file.write(sambamba_version)
+ sambamba_file.close()
else:
logger.error('Missing sambamba')
raise Exception('Missing sambamba')
@@ -76,6 +97,15 @@ def check_tools():
bedtools_path = shutil.which("bedtools")
if bedtools_path:
logger.info('Found bedtools: %s', bedtools_path)
+
+ # Get Version
+ bedtools_version_command = "bedtools --version"
+ bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
+
+ # Write to file
+ bedtools_file = open("version_bedtools.txt", "wb")
+ bedtools_file.write(bedtools_version)
+ bedtools_file.close()
else:
logger.error('Missing bedtools')
raise Exception('Missing bedtools')
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index a1f8161cb4ee71885719d954e9ddf25428499d11..3ba41dc9cd616759754abaaa6abc390362f00ab0 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -70,6 +70,18 @@ def check_tools():
bwa_path = shutil.which("bwa")
if bwa_path:
logger.info('Found bwa: %s', bwa_path)
+
+ # Get Version
+ bwa_version_command = "bwa"
+ try:
+ subprocess.check_output(bwa_version_command, shell=True, stderr=subprocess.STDOUT)
+ except subprocess.CalledProcessError as e:
+ bwa_version = e.output
+
+ # Write to file
+ bwa_file = open("version_bwa.txt", "wb")
+ bwa_file.write(bwa_version)
+ bwa_file.close()
else:
logger.error('Missing bwa')
raise Exception('Missing bwa')
@@ -77,6 +89,15 @@ def check_tools():
samtools_path = shutil.which("samtools")
if samtools_path:
logger.info('Found samtools: %s', samtools_path)
+
+ # Get Version
+ samtools_version_command = "samtools --version"
+ samtools_version = subprocess.check_output(samtools_version_command, shell=True)
+
+ # Write to file
+ samtools_file = open("version_samtools.txt", "wb")
+ samtools_file.write(samtools_version)
+ samtools_file.close()
else:
logger.error('Missing samtools')
raise Exception('Missing samtools')
diff --git a/workflow/scripts/motif_search.py b/workflow/scripts/motif_search.py
index 02e316f67a7bdaf26541ca864ceebfcac50e120a..0c2e3f8c4efdefccaa016dfb4e3b75569ce0f5fa 100644
--- a/workflow/scripts/motif_search.py
+++ b/workflow/scripts/motif_search.py
@@ -6,6 +6,7 @@ import os
import argparse
import logging
import shutil
+import subprocess
from multiprocessing import Pool
import pandas as pd
import utils
@@ -63,6 +64,15 @@ def check_tools():
meme_path = shutil.which("meme")
if meme_path:
logger.info('Found meme: %s', meme_path)
+
+ # Get Version
+ memechip_version_command = "meme-chip --version"
+ memechip_version = subprocess.check_output(memechip_version_command, shell=True)
+
+ # Write to file
+ meme_file = open("version_memechip.txt", "wb")
+ meme_file.write("Version %s" % (memechip_version))
+ meme_file.close()
else:
logger.error('Missing meme')
raise Exception('Missing meme')
@@ -70,6 +80,15 @@ def check_tools():
bedtools_path = shutil.which("bedtools")
if bedtools_path:
logger.info('Found bedtools: %s', bedtools_path)
+
+ # Get Version
+ bedtools_version_command = "bedtools --version"
+ bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
+
+ # Write to file
+ bedtools_file = open("version_bedtools.txt", "wb")
+ bedtools_file.write(bedtools_version)
+ bedtools_file.close()
else:
logger.error('Missing bedtools')
raise Exception('Missing bedtools')
diff --git a/workflow/scripts/overlap_peaks.py b/workflow/scripts/overlap_peaks.py
index 61f0c2e6d11553e54bd9cf5a1cc5c629fa9acb5c..71438f779ab96695ead05a5653221ae99f5b3f6a 100644
--- a/workflow/scripts/overlap_peaks.py
+++ b/workflow/scripts/overlap_peaks.py
@@ -49,6 +49,15 @@ def check_tools():
bedtools_path = shutil.which("bedtools")
if bedtools_path:
logger.info('Found bedtools: %s', bedtools_path)
+
+ # Get Version
+ bedtools_version_command = "bedtools --version"
+ bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
+
+ # Write to file
+ bedtools_file = open("version_bedtools.txt", "wb")
+ bedtools_file.write(bedtools_version)
+ bedtools_file.close()
else:
logger.error('Missing bedtools')
raise Exception('Missing bedtools')
diff --git a/workflow/scripts/software_report.py b/workflow/scripts/software_report.py
new file mode 100644
index 0000000000000000000000000000000000000000..1b0a3b831fe80c76a99f1c2242b4ec7c89bcf12b
--- /dev/null
+++ b/workflow/scripts/software_report.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from __future__ import print_function
+from collections import OrderedDict
+import re
+
+regexes = {
+ 'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
+ 'Cutadapt': ['version_cutadapt.txt', r"Version (\S+)"],
+ 'BWA': ['version_bwa.txt', r"Version: (\S+)"],
+ 'Samtools': ['version_samtools.txt', r"samtools (\S+)"],
+ 'Sambamba': ['version_sambamba.txt', r"sambamba (\S+)"],
+ 'BEDTools': ['version_bedtools.txt', r"bedtools v(\S+)"],
+ 'R': ['version_r.txt', r"R version (\S+)"],
+ 'SPP': ['version_spp.txt', r"\[1\] ‘(1.14)’"],
+ 'MACS2': ['version_macs.txt', r"macs2 (\S+)"],
+ 'bedGraphToBigWig': ['version_bedGraphToBigWig.txt', r"bedGraphToBigWig v (\S+)"],
+ 'ChIPseeker': ['version_ChIPseeker.txt', r"Version (\S+)\""],
+ 'MEME-ChIP': ['version_memechip.txt', r"Version (\S+)"],
+ 'DiffBind': ['version_DiffBind.txt', r"Version (\S+)"],
+ 'deepTools': ['version_deeptools.txt', r"deeptools (\S+)"],
+}
+
+results = OrderedDict()
+results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
+results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
+results['BWA'] = '<span style="color:#999999;\">N/A</span>'
+results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
+results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
+results['BWA'] = '<span style="color:#999999;\">N/A</span>'
+results['Samtools'] = '<span style="color:#999999;\">N/A</span>'
+results['Sambamba'] = '<span style="color:#999999;\">N/A</span>'
+results['BEDTools'] = '<span style="color:#999999;\">N/A</span>'
+results['R'] = '<span style="color:#999999;\">N/A</span>'
+results['SPP'] = '<span style="color:#999999;\">N/A</span>'
+results['MACS2'] = '<span style="color:#999999;\">N/A</span>'
+results['bedGraphToBigWig'] = '<span style="color:#999999;\">N/A</span>'
+results['ChIPseeker'] = '<span style="color:#999999;\">N/A</span>'
+results['MEME-ChIP'] = '<span style="color:#999999;\">N/A</span>'
+results['DiffBind'] = '<span style="color:#999999;\">N/A</span>'
+results['deepTools'] = '<span style="color:#999999;\">N/A</span>'
+
+# Search each file using its regex
+for k, v in regexes.items():
+ with open(v[0]) as x:
+ versions = x.read()
+ match = re.search(v[1], versions)
+ if match:
+ results[k] = "v{}".format(match.group(1))
+
+# Dump to YAML
+print(
+ '''
+ id: 'BICF ChIP-seq Analaysis'
+ section_name: 'BICF ChIP-seq Analaysis Software Versions'
+ section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
+ plot_type: 'html'
+ description: 'are collected at run time from the software output.'
+ data: |
+ <dl class="dl-horizontal">
+ '''
+)
+for k,v in results.items():
+ print(" <dt>{}</dt><dd>{}</dd>".format(k,v))
+print(" </dl>")
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index e31ec938b6d7e0ef5570afc394c98a365041f863..e4461d5daf3f9f5e4e99552cd86a50d67f44778c 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -54,6 +54,15 @@ def check_tools():
trimgalore_path = shutil.which("trim_galore")
if trimgalore_path:
logger.info('Found trimgalore: %s', trimgalore_path)
+
+ # Get Version
+ trim_version_command = "trim_galore --version"
+ trimgalore_version = subprocess.check_output(trim_version_command, shell=True)
+
+ # Write to file
+ trimgalore_file = open("version_trimgalore.txt", "wb")
+ trimgalore_file.write(trimgalore_version)
+ trimgalore_file.close()
else:
logger.error('Missing trimgalore')
raise Exception('Missing trimgalore')
@@ -61,6 +70,15 @@ def check_tools():
cutadapt_path = shutil.which("cutadapt")
if cutadapt_path:
logger.info('Found cutadapt: %s', cutadapt_path)
+
+ # Get Version
+ cutadapt_version_command = "cutadapt --version"
+ cutadapt_version = subprocess.check_output(cutadapt_version_command, shell=True)
+
+ # Write to file
+ cutadapt_file = open("version_cutadapt.txt", "wb")
+ cutadapt_file.write("Version %s" % (cutadapt_version))
+ cutadapt_file.close()
else:
logger.error('Missing cutadapt')
raise Exception('Missing cutadapt')
diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py
index ac2ff65f7f06707e892e1033106dc2219ecb96cd..eddfc0d23eeacd9e30ca3540802943172535fc22 100644
--- a/workflow/scripts/xcor.py
+++ b/workflow/scripts/xcor.py
@@ -5,6 +5,7 @@
import os
import argparse
import shutil
+import subprocess
import logging
from multiprocessing import cpu_count
import utils
@@ -59,10 +60,35 @@ def check_tools():
r_path = shutil.which("R")
if r_path:
logger.info('Found R: %s', r_path)
+
+ # Get Version
+ r_version_command = "R --version"
+ r_version = subprocess.check_output(r_version_command, shell=True)
+
+ # Write to file
+ r_file = open("version_r.txt", "wb")
+ r_file.write(r_version)
+ r_file.close()
else:
logger.error('Missing R')
raise Exception('Missing R')
+ phantompeak_path = shutil.which("run_spp.R")
+ if phantompeak_path:
+ logger.info('Found phantompeak: %s', phantompeak_path)
+
+ # Get Version
+ spp_version_command = "R -e \"packageVersion('spp')\""
+ spp_version = subprocess.check_output(spp_version_command, shell=True, stderr=subprocess.STDOUT)
+
+ # Write to file
+ spp_file = open("version_spp.txt", "wb")
+ spp_file.write(spp_version)
+ spp_file.close()
+ else:
+ logger.error('Missing phantompeak')
+ raise Exception('Missing phantompeak')
+
def xcor(tag, paired):
'''Use spp to calculate cross-correlation stats.'''