Commit ca6b9015 authored by Mikaël Salson's avatar Mikaël Salson

Makefile: Build an archive for the dataset or manually curated real V(D)J sequences

parent 80eea121
......@@ -14,6 +14,10 @@ SHOULD_LOCUS=$(wildcard should-vdj-tests/*.should-locus.fa)
REPORTS_PATH := $(patsubst %/Makefile,%,$(abspath $(lastword $(MAKEFILE_LIST))))/../../reports
VALGRIND=valgrind -v --tool=memcheck --leak-check=full --show-reachable=yes --undef-value-errors=yes --track-origins=yes --xml=yes --xml-file="$$(mktemp "$(REPORTS_PATH)/valgrind.xml.XXXXXX")"
#should-vdj that should not be published in our public curated dataset (just internal tests)
EXCLUDE_SHOULD_VDJ=bug20151006-rc.should-vdj.fa cdr3-indels.should-vdj.fa ext-nucleotides-N.should-vdj.fa segment_simul.should-vdj.fa
SHOULD_VDJ_ARCHIVE:=$(filter-out $(addprefix should-vdj-tests/,$(EXCLUDE_SHOULD_VDJ)), $(SHOULD_VDJ))
DATE=$(shell date +%Y-%m-%d--%H:%M:%S)
SNAPSHOTS_DIR=./snapshots
SNAPSHOT=$(SNAPSHOTS_DIR)/snapshot-log--$(DATE)
......@@ -61,6 +65,15 @@ shouldvdj_with_rc_merged:
cat $(SHOULD_VDJ) > should-vdj-tests/should-vdj.merged.fa
python should-vdj-to-tap.py -r should-vdj-tests/should-vdj.merged.fa
shouldvdj_archive: should-vdj.zip
should-vdj.zip: $(SHOULD_VDJ_ARCHIVE)
$(eval tmpdir := $(shell mktemp -d))
mkdir $(tmpdir)/should-vdj
cp --parents --preserve $(SHOULD_VDJ_ARCHIVE) $(tmpdir)
sed -ri 's/\s*BUG//' $(tmpdir)/should-vdj-tests/*
cwd=`pwd` && cd $(tmpdir) && zip $$cwd/$@ $(SHOULD_VDJ_ARCHIVE)
rm -rf $(tmpdir)
%.tap: %.should-get force
./should-to-tap.sh $<
......
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