Commit b1f2df18 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/3003-make-sequence' into 'dev'

Add LIL-L4 demo sequences, 'make demo'

See merge request !147
parents cf042c7c a0baa303
Pipeline #15636 passed with stages
in 26 seconds
......@@ -44,7 +44,7 @@ unit_server:
data:
$(MAKE) -C algo/tests/data
germline browser server: %:
demo germline browser server: %:
$(MAKE) -C $@
cleanall: clean
......@@ -53,7 +53,7 @@ cleanall: clean
$(MAKE) -C $(VIDJIL_ALGO_SRC) cleanall
$(MAKE) -C server cleanall
.PHONY: all test should clean cleanall distrib data germline unit_coverage should_coverage coverage data germline browser server doc algo
.PHONY: all test should clean cleanall distrib data demo germline unit_coverage should_coverage coverage data germline browser server doc algo
......
......@@ -3,7 +3,8 @@ DATA=Stanford_S22.fasta Stanford_S22.rc.fasta chimera-fake-VJ-trim.g
all: $(DATA)
Stanford_S22.fasta:
cd ../../../demo ; sh get-sequences
$(MAKE) -C ../../../demo
rm -f Stanford_S22*.fasta
ln -sv ../../../demo/Stanford_S22*.fasta .
Stanford_S22.rc.fasta: Stanford_S22.fasta
......
FILES=LIL-L4.fastq.gz Stanford_S22.tar.gz Stanford_S22.fasta Stanford_S22.rc.fasta
all: $(FILES)
$(FILES):
sh get-sequences
clean:
rm -f $(FILES)
.PHONY: all clean
#!/bin/sh
echo <<EOF
Please pay attention that the Stanford_S22 dataset comes from Boyd,
S. D., et al. Individual variation in the germline Ig gene repertoire inferred
from variable region gene rearrangements. J Immunol, 184(12), 6986–92.
Downloading public data
- Stanford_S22 dataset from
Boyd, S. D., et al. Individual variation in the germline Ig gene repertoire inferred
from variable region gene rearrangements. J Immunol, 184(12), 6986–92.
- LIL-L4 dataset from
Giraud, Salson, et al. Fast multiclonal clusterization of V(D)J recombinations
from high-throughput sequencing. BMC Genomics 2014, 15:409.
EOF
wget -q -O- http://www.vidjil.org/seqs/Stanford_S22.tar.gz | tar xvzf -
wget -nc -q http://www.vidjil.org/seqs/Stanford_S22.tar.gz
tar xvzf Stanford_S22.tar.gz
wget -nc -q --show-progress -O LIL-L4.fastq.gz https://db.vidjil.org/vidjil/patient/download/sequence_file.data_file.89a7ad1ac0e2c6fa.4c313530303132352e496f6e5870726573735f3039362e66617374712e677a.gz
status=$?
# wget -nc -O exits with 1 when file already exists but thit is is not an
# error and should not fail the Makefile!
if [ $status -eq 1 ]; then
exit 0
else
exit $status
fi
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment