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Makefile.am
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Makefile.am
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ACLOCAL_AMFLAGS = -I m4
nodist_bin_SCRIPTS = \
pigx-bsseq
dist_pkglibexec_SCRIPTS = \
BSseq_pipeline.py
pkglibexec_scriptsdir = $(pkglibexecdir)/scripts
dist_pkglibexec_scripts_SCRIPTS = \
scripts/fetch_refGene.R \
scripts/func_defs.py \
scripts/ideoDMC.R \
scripts/integrate2finalreport.R \
scripts/multireport_functions.R \
scripts/report_functions.R
pkglibexec_rulesdir = $(pkglibexecdir)/rules
dist_pkglibexec_rules_SCRIPTS = \
rules/post_mapping.rules \
rules/samtools.rules \
rules/SRA2fastq
pkgdata_report_templatesdir = $(pkgdatadir)/report_templates
dist_pkgdata_report_templates_SCRIPTS = \
report_templates/annotation.report.Rmd \
report_templates/annotation.report.diff.meth.Rmd \
report_templates/diffmeth.report.Rmd \
report_templates/index.Rmd \
report_templates/methCall.report.Rmd \
report_templates/methseg.report.Rmd \
report_templates/pigx_bsseq_logo.html \
report_templates/references.Rmd \
report_templates/sessioninfo.Rmd \
report_templates/reports.bib
dist_pkgdata_DATA = \
etc/programs.json \
etc/pretty.txt
dist_doc_DATA = \
README.md
EXTRA_DIST = \
test/genome/myref_hg38_chr1_7291263_7302041.fasta \
test/in/PE_1.fq.gz \
test/in/PE_2.fq.gz \
test/in/SE_techrep1.fq.gz \
test/in/SE_techrep2.fq.gz \
test/Tablesheet.txt
TESTS = test.sh
CLEANFILES = $(nodist_bin_SCRIPTS) report_templates/pigx_bsseq_logo.html config.json
# This is a hack to embed the logo in the html file.
report_templates/pigx_bsseq_logo.html:
@sed "s|#:MAKE|$(shell base64 -w0 < images/Logo_PiGx.png)|" report_templates/pigx_bsseq_logo.html.in > $@