[med-svn] [adapterremoval] 01/01: Adapt to pIRS 2.0.1
Andreas Tille
tille at debian.org
Tue Aug 9 14:45:25 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository adapterremoval.
commit bc0aa4afa244c86d4cb778780f0b783de32f3718
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 9 16:42:46 2016 +0200
Adapt to pIRS 2.0.1
---
debian/patches/adapt-benchmarking.patch | 78 +++++++++++++++++++++++-----
debian/patches/do_not_gunzip.patch | 21 ++++++++
debian/patches/reduce_benchmark_length.patch | 21 ++++----
debian/patches/series | 1 +
4 files changed, 98 insertions(+), 23 deletions(-)
diff --git a/debian/patches/adapt-benchmarking.patch b/debian/patches/adapt-benchmarking.patch
index 7bb5e87..56e69ff 100644
--- a/debian/patches/adapt-benchmarking.patch
+++ b/debian/patches/adapt-benchmarking.patch
@@ -156,11 +156,11 @@
# -c 0 = uncompressed output
- if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" -i "${REFSEQ}" -c 0 -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
-+ if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c text -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
++ if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c gzip -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
> "${DST}/reads.stdout" 2> "${DST}/reads.stderr";
then
echo "Error simulated reads ..." > /dev/stderr
-@@ -813,7 +833,7 @@ function benchmark_se()
+@@ -813,14 +833,16 @@ function benchmark_se()
SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
@@ -168,8 +168,22 @@
+ RESULTS="$results/se/${readlen}_${run_n}"
# -mm 3 corresponds to AR 2.x defaults
- echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \
-@@ -901,7 +921,7 @@ function benchmark_se()
+- echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \
+- "${RESULTS}/adapterremoval1x_mm3" \
+- "${SIMULATED_INFO}" \
+- --file1 "${SIMULATED_MATE1}" \
+- --mm 3
++ if [ "${EXEC_ADAPTERREMOVAL1x}" != "" } ; then
++ echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \
++ "${RESULTS}/adapterremoval1x_mm3" \
++ "${SIMULATED_INFO}" \
++ --file1 "${SIMULATED_MATE1}" \
++ --mm 3
++ fi
+
+ # -mm 3 --minadapteroverlap 3 (test)
+ echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \
+@@ -901,7 +923,7 @@ function benchmark_se()
done
done
@@ -178,7 +192,7 @@
}
-@@ -921,7 +941,7 @@ function benchmark_pe()
+@@ -921,17 +943,19 @@ function benchmark_pe()
SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
@@ -187,7 +201,25 @@
DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-@@ -997,7 +1017,7 @@ function benchmark_pe()
+ # -mm 3 corresponds to AR 2.x defaults
+- echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL1x} 1 \
+- "${RESULTS}/adapterremoval1x_mm3" \
+- "${SIMULATED_INFO}" \
+- --file1 "${SIMULATED_MATE1}" \
+- --file2 "${SIMULATED_MATE2}" \
+- --mm 3
++ if [ "${EXEC_ADAPTERREMOVAL1x}" != "" ] ; then
++ echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL1x} 1 \
++ "${RESULTS}/adapterremoval1x_mm3" \
++ "${SIMULATED_INFO}" \
++ --file1 "${SIMULATED_MATE1}" \
++ --file2 "${SIMULATED_MATE2}" \
++ --mm 3
++ fi
+
+ for nthreads in $(seq 1 ${MAX_THREADS});
+ do
+@@ -997,7 +1021,7 @@ function benchmark_pe()
done
done
@@ -196,7 +228,7 @@
}
-@@ -1017,7 +1037,7 @@ function benchmark_collapse()
+@@ -1017,17 +1041,19 @@ function benchmark_collapse()
SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
@@ -205,7 +237,25 @@
DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-@@ -1063,7 +1083,7 @@ function benchmark_collapse()
+ # -mm 3 corresponds to AR 2.x defaults
+- echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL1x} 1 \
+- "${RESULTS}/adapterremoval1x_mm3" \
+- "${SIMULATED_INFO}" \
+- --file1 "${SIMULATED_MATE1}" \
+- --file2 "${SIMULATED_MATE2}" \
+- --mm 3 --collapse
++ if [ "${EXEC_ADAPTERREMOVAL1x}" != "" ] ; then
++ echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL1x} 1 \
++ "${RESULTS}/adapterremoval1x_mm3" \
++ "${SIMULATED_INFO}" \
++ --file1 "${SIMULATED_MATE1}" \
++ --file2 "${SIMULATED_MATE2}" \
++ --mm 3 --collapse
++ fi
+
+ for nthreads in $(seq 1 ${MAX_THREADS});
+ do
+@@ -1063,7 +1089,7 @@ function benchmark_collapse()
done
done
@@ -214,7 +264,7 @@
}
-@@ -1084,7 +1104,7 @@ function benchmark_mixed_se
+@@ -1084,7 +1110,7 @@ function benchmark_mixed_se
SIMULATED_MATE1="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_1.fq"
SIMULATED_MATE2="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_2.fq"
SIMULATED_INFO="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}.read.info"
@@ -223,7 +273,7 @@
DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
AR_PREFIX="${RESULTS}/adapterremoval2x"
-@@ -1139,7 +1159,7 @@ function benchmark_mixed_se
+@@ -1139,7 +1165,7 @@ function benchmark_mixed_se
done
done
@@ -232,7 +282,7 @@
}
-@@ -1159,7 +1179,7 @@ function benchmark_mixed_pe
+@@ -1159,7 +1185,7 @@ function benchmark_mixed_pe
SIMULATED_MATE1="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_1.fq"
SIMULATED_MATE2="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_2.fq"
SIMULATED_INFO="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}.read.info"
@@ -241,7 +291,7 @@
DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-@@ -1204,7 +1224,7 @@ function benchmark_mixed_pe
+@@ -1204,7 +1230,7 @@ function benchmark_mixed_pe
done
done
@@ -250,7 +300,7 @@
}
-@@ -1224,7 +1244,7 @@ function benchmark_adapter_id
+@@ -1224,7 +1250,7 @@ function benchmark_adapter_id
SIMULATED_MATE1="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}_1.fq"
SIMULATED_MATE2="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}_2.fq"
SIMULATED_INFO="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}.read.info"
@@ -259,7 +309,7 @@
run_minion "${RESULTS}/minion" \
"${SIMULATED_MATE1}" \
-@@ -1236,13 +1256,14 @@ function benchmark_adapter_id
+@@ -1236,13 +1262,14 @@ function benchmark_adapter_id
done
done
diff --git a/debian/patches/do_not_gunzip.patch b/debian/patches/do_not_gunzip.patch
new file mode 100644
index 0000000..112a408
--- /dev/null
+++ b/debian/patches/do_not_gunzip.patch
@@ -0,0 +1,21 @@
+--- a/benchmark/benchmark.sh
++++ b/benchmark/benchmark.sh
+@@ -308,14 +308,16 @@ function simulate_reads()
+ mkdir -p "${DST}/"
+
+ # -c 0 = uncompressed output
+- if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c gzip -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
++ if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c text -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
+ > "${DST}/reads.stdout" 2> "${DST}/reads.stderr";
+ then
+ echo "Error simulated reads ..." > /dev/stderr
+ exit 1
+ fi
+
+- gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz"
++ if [ -e "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz" ] ; then
++ gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz"
++ fi
+ ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_1.fq" "${DST}_1.fq"
+ ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_2.fq" "${DST}_2.fq"
+ ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}.read.info" "${DST}.read.info"
diff --git a/debian/patches/reduce_benchmark_length.patch b/debian/patches/reduce_benchmark_length.patch
index 0098336..4b0c8f0 100644
--- a/debian/patches/reduce_benchmark_length.patch
+++ b/debian/patches/reduce_benchmark_length.patch
@@ -1,14 +1,5 @@
--- a/benchmark/benchmark.sh
+++ b/benchmark/benchmark.sh
-@@ -34,7 +34,7 @@ NUM_REPLICATES=10
- # Read lengths to examine
- # Lengths > 100 use an interpolated profile, and should therefore not be used
- # to estimate anything other than runtime (see 'simulate_reads').
--READ_LENGTHS=(100 200)
-+READ_LENGTHS=(100)
-
- # Insert sizes of reads to simulate for adapter ID
- ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350))
@@ -44,7 +44,7 @@ ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350
MAX_THREADS=4
@@ -18,3 +9,15 @@
results=$(mktemp -d /tmp/adapter-benchmark.XXXXXX)
echo "*** Results will be found in $results ***"
+@@ -266,8 +266,10 @@ function fetch_reference()
+ echo "" > /dev/stderr
+ # wget -O $results/reference.fasta.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz
+ # gunzip $results/reference.fasta.gz
++ cp -a /usr/share/doc/pirs/examples/pirs/ref_seq.fa.gz $results/reference.fasta.gz
++ gunzip $results/reference.fasta.gz
+ echo "FIXME!!!!!"
+-cp -a /tmp/adapter-benchmark/reference.fasta $results
++#cp -a /tmp/adapter-benchmark/reference.fasta $results
+ fi
+
+
diff --git a/debian/patches/series b/debian/patches/series
index fb2682a..ec30ca0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
hardening.patch
adapt-benchmarking.patch
reduce_benchmark_length.patch
+do_not_gunzip.patch
--
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