Commit 61ae0b39 authored by Christian Arnold's avatar Christian Arnold

various small issues, improved macOS compatibility

parent a2e7e3a2
......@@ -98,9 +98,9 @@ A working ``R`` installation is needed and a number of packages from either CRAN
.. code-block:: R
install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "gridExtra", "scales", "jsonlite", "RcolorBrewer", "rlist", "ggrepel", "lsr", "modeest", "locfdr", "boot"))
install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "gridExtra", "scales", "jsonlite", "RColorBrewer", "rlist", "ggrepel", "lsr", "modeest", "locfdr", "boot"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("limma", "vsn", "csaw", "DESeq2", "DiffBind", "geneplotter", "Rsamtools"))
biocLite(c("limma", "vsn", "csaw", "DESeq2", "EDASeq", "DiffBind", "geneplotter", "Rsamtools"))
......
......@@ -17,4 +17,4 @@ echo "# INCREASING THE NUMBER OF CORES SPEEDS UP THE ANALYSIS #"
echo "#########################################################"
# Real run, using 2 cores
snakemake --snakefile ../../src/Snakefile --cores 2 --configfile config.json --timestamp --directory . --forceall
snakemake --snakefile ../../src/Snakefile --cores 2 --configfile config.json --timestamp --directory .
......@@ -215,7 +215,7 @@ if config["peaks"]["consensusPeaks"]:
if not os.path.isfile(filenameCur):
raise IOError("File \"" + filenameCur + "\" not found.")
# Check if it contains scientific notification
# the || true in the end ensures the exit status of grep is 0, because this would raise an error otherwise
# the || true in the end ensures the exit status of is 0, because this would raise an error otherwise
nHits = int(subprocess.check_output('grep -c "e+" ' + config["peaks"]["consensusPeaks"] + " || true", shell=True))
if nHits > 0:
raise AssertionError("File " + config["peaks"]["consensusPeaks"] + " contains at least one line with the scientific notation (e+). This will cause errors in subsequent steps. Check the file and transform all \"e+\" coordinates.")
......@@ -515,7 +515,7 @@ rule calcNucleotideContent:
params: refGenome = config["additionalInputFiles"]["refGenome_fasta"]
shell:
"""
zcat {input.motifsBed} | grep "^{wildcards.perm}\\t" | awk '{{OFS="\\t"}};{{print $3,$4,$5,$6,$2}}' | gzip -f > {output.bedTemp} &&
zgrep "$(printf '^{wildcards.perm}\\t')" {input.motifsBed} | awk '{{OFS="\\t"}};{{print $3,$4,$5,$6,$2}}' | gzip -f > {output.bedTemp} &&
bedtools nuc -fi {params.refGenome} -bed {output.bedTemp} | gzip -f > {output.bed}
"""
......
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