[med-svn] [art-nextgen-simulation-tools] 03/03: Add data package and run test suite
Andreas Tille
tille at debian.org
Tue Feb 16 19:09:51 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository art-nextgen-simulation-tools.
commit 7081a4c148bfc54b8e7eacfa575b16b929268486
Author: Andreas Tille <tille at debian.org>
Date: Tue Feb 16 19:20:00 2016 +0100
Add data package and run test suite
---
debian/README.test | 7 ++++
debian/art-nextgen-simulation-tools-data.examples | 1 +
debian/art-nextgen-simulation-tools-data.install | 1 +
debian/control | 28 +++++++++++++++-
debian/patches/fix-test-comparison.patch | 18 +++++++++++
debian/patches/series | 1 +
debian/rules | 39 +++++++++++++----------
7 files changed, 78 insertions(+), 17 deletions(-)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..fc851bf
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,7 @@
+
+
+In run_test_examples_SOLiD.sh
+
+ ../art_SOLiD -A s -s amplicon_reference.fa ./amp_single 25 100
+
+takes some time ...
diff --git a/debian/art-nextgen-simulation-tools-data.examples b/debian/art-nextgen-simulation-tools-data.examples
new file mode 100644
index 0000000..2b19e25
--- /dev/null
+++ b/debian/art-nextgen-simulation-tools-data.examples
@@ -0,0 +1 @@
+examples/*.fa
diff --git a/debian/art-nextgen-simulation-tools-data.install b/debian/art-nextgen-simulation-tools-data.install
new file mode 100644
index 0000000..c5dcf2d
--- /dev/null
+++ b/debian/art-nextgen-simulation-tools-data.install
@@ -0,0 +1 @@
+*profile* usr/share/art-nextgen-simulation-tools
diff --git a/debian/control b/debian/control
index af112f2..11a78bc 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,8 @@ Homepage: http://www.niehs.nih.gov/research/resources/software/biostatistics/art
Package: art-nextgen-simulation-tools
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ art-nextgen-simulation-tools-data
Description: simulation tools to generate synthetic next-generation sequencing reads
ART is a set of simulation tools to generate synthetic next-generation
sequencing reads. ART simulates sequencing reads by mimicking real
@@ -34,3 +35,28 @@ Description: simulation tools to generate synthetic next-generation sequencing r
alignment or UCSC BED file format. ART can be used together with genome
variants simulators (e.g. VarSim) for evaluating variant calling tools
or methods.
+
+Package: art-nextgen-simulation-tools-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: simulation tools to generate synthetic next-generation sequencing reads
+ ART is a set of simulation tools to generate synthetic next-generation
+ sequencing reads. ART simulates sequencing reads by mimicking real
+ sequencing process with empirical error models or quality profiles
+ summarized from large recalibrated sequencing data. ART can also
+ simulate reads using user own read error model or quality profiles. ART
+ supports simulation of single-end, paired-end/mate-pair reads of three
+ major commercial next-generation sequencing platforms: Illumina's
+ Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to
+ test or benchmark a variety of method or tools for next-generation
+ sequencing data analysis, including read alignment, de novo assembly,
+ SNP and structure variation discovery. ART was used as a primary tool
+ for the simulation study of the 1000 Genomes Project . ART is
+ implemented in C++ with optimized algorithms and is highly efficient in
+ read simulation. ART outputs reads in the FASTQ format, and alignments
+ in the ALN format. ART can also generate alignments in the SAM
+ alignment or UCSC BED file format. ART can be used together with genome
+ variants simulators (e.g. VarSim) for evaluating variant calling tools
+ or methods.
+ .
+ This package contains profile data for art-nextgen-simulation-tools.
diff --git a/debian/patches/fix-test-comparison.patch b/debian/patches/fix-test-comparison.patch
new file mode 100644
index 0000000..dd696cb
--- /dev/null
+++ b/debian/patches/fix-test-comparison.patch
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 16 Feb 2016 15:19:22 +0100
+Description: There is one single difference between the created
+ sam files which is the different command line. This patch is
+ removing the diff and comparing files that should be really equal.
+
+--- a/examples/run_test_examples_454.sh
++++ b/examples/run_test_examples_454.sh
+@@ -31,6 +31,7 @@ $art_454 -a -s -B ./amplicon_reference.f
+ $art_454 -a -s -r 777 ./testSeq.fa ./single_454_t1 10
+ $art_454 -a -s -r 777 ./testSeq.fa ./single_454_t2 10
+ # compare difference
+-echo "compare difference of two simulation datasets"
+-diff single_454_t1.sam single_454_t2.sam
++echo "compare difference of two simulation datasets after normalising known difference"
++sed 's?^\(@PG.*testSeq\.fa \./single_454_t\)2?\11?' single_454_t2.sam > single_454_t2_normalised.sam
++diff single_454_t1.sam single_454_t2_normalised.sam
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..477d052
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix-test-comparison.patch
diff --git a/debian/rules b/debian/rules
index 540d578..641c384 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,22 +1,29 @@
#!/usr/bin/make -f
-# DH_VERBOSE := 1
-
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG := $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables, you can
-# include /usr/share/dpkg/default.mk
-# and use what is set there.
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+DATAPKG := $(DEBPKGNAME)-data
%:
dh $@ --with autoreconf
-#get-orig-source:
-# . debian/get-orig-source
+override_dh_auto_test:
+ifneq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
+ echo 'skip testing due to DEB_BUILD_OPTIONS="$(DEB_BUILD_OPTIONS)"'
+else
+ set -e && \
+ cd examples && \
+ ./run_test_examples_454.sh && \
+ ./run_test_examples_SOLiD.sh && \
+ ./run_test_examples_illumina.sh
+ rm -f *.aln *.fq *.bed *.map *.sam *.stat
+endif
+
+override_dh_installexamples-indep:
+ dh_installexamples -i
+ mkdir -p debian/$(DATAPKG)/usr/share/doc/$(DEBPKGNAME)
+ mv debian/$(DATAPKG)/usr/share/doc/$(DATAPKG)/examples debian/$(DATAPKG)/usr/share/doc/$(DEBPKGNAME)
+ for ex in examples/run_test_examples_*.sh ; do \
+ sed -e 's?=\.\./?/usr/bin/?' -e 's?^\.\./?/usr/bin/?' $$ex > debian/$(DATAPKG)/usr/share/doc/$(DEBPKGNAME)/examples/`basename $$ex` ; \
+ done
+
+
\ No newline at end of file
--
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