[med-svn] [Git][med-team/sra-sdk][master] 4 commits: Start work on sra-sdk 2.10.9+dfsg-2.

[Aaron M. Ucko]

Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk


Commits:
c9ecc36c by Aaron M. Ucko at 2021-02-04T20:34:44-05:00
Start work on sra-sdk 2.10.9+dfsg-2.

- - - - -
0477964a by Aaron M. Ucko at 2021-02-04T20:35:54-05:00
run-unit-test: Give up for now on {abi,fastq,illumina,sff}-load.

All four rely deeply on retired VDB functionality that would be
too awkward to reintroduce.

- - - - -
7a202959 by Aaron M. Ucko at 2021-02-04T20:38:06-05:00
New patch skip_broken_loaders.patch.

Stop building or trying to install anything from tools/sra-load, to
avoid leading users on.

- - - - -
4acc0f4f by Aaron M. Ucko at 2021-02-04T20:38:52-05:00
Finalize sra-sdk 2.10.9+dfsg-2 for unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/skip_broken_loaders.patch
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium
+
+  * run-unit-test: Give up for now on {abi,fastq,illumina,sff}-load.
+    All four rely deeply on retired VDB functionality that would be
+    too awkward to reintroduce.
+  * skip_broken_loaders.patch (new): Likewise stop building or trying to
+    install anything from tools/sra-load, to avoid leading users on.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Thu, 04 Feb 2021 20:38:51 -0500
+
 sra-sdk (2.10.9+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/patches/series
=====================================
@@ -20,3 +20,4 @@ python3
 use_exposed_headers.patch
 use_unversioned_tools.patch
 #reenable_legacy_schema_in_sra_load.patch
+skip_broken_loaders.patch


=====================================
debian/patches/skip_broken_loaders.patch
=====================================
@@ -0,0 +1,21 @@
+--- a/tools/Makefile
++++ b/tools/Makefile
+@@ -60,7 +60,6 @@ SUBDIRS =             \
+ 	vcf-loader        \
+ 	copycat           \
+ 	fasterq-dump      \
+-	sra-load          \
+ 	ccextract         \
+ 	pacbio-load       \
+ 	fuse              \
+--- a/build/Makefile.install
++++ b/build/Makefile.install
+@@ -40,7 +40,7 @@ include $(TOP)/build/Makefile.$(OS)
+ include $(TOP)/build/Makefile.tools
+ ifeq (1,$(HAVE_HDF5))
+         TOOLS_TO_COPY += pacbio-load
+-        TOOLS_TO_COPY += pacbio-loadxml
++        TOOLS_TO_COPY_OPTIONAL += pacbio-loadxml
+ endif
+ 
+ # unset outside defined variables


=====================================
debian/tests/run-unit-test
=====================================
@@ -46,18 +46,18 @@ latf-load -p LS454 --quality PHRED_33 -o SRR2042184 SRR2042184_1.fastq
 echo ">>>>>Running kar..."
 kar -c SRR2042184.sra -d SRR2042184
 [ -s SRR2042184.sra ]
-echo ">>>>>Running fastq-load..."
-fastq-load -r meta/SRR6650398_fastq_run.xml -e meta/SRR6650398_experiment.xml -o SRR6650398
-rm -r SRR2042184 SRR6650398 SRR2042184.sra SRR2042184_1.fastq SRR6650398_1.fastq
+# echo ">>>>>Running fastq-load..."
+# fastq-load -r meta/SRR6650398_fastq_run.xml -e meta/SRR6650398_experiment.xml -o SRR6650398
+rm -rf SRR2042184 SRR6650398 SRR2042184.sra SRR2042184_1.fastq SRR6650398_1.fastq
 
 echo ">>>>>Running abi-dump..."
 abi-dump -F SRR7032226
 # make sequence descriptor to look like from SOLiD
 sed 's/>1/>1_11_1111_F3/' SRR7032226_F3.csfasta > SRR7032226_F3e.csfasta
 sed 's/>1/>1_11_1111_F3/' SRR7032226_F3_QV.qual > SRR7032226_F3_QVe.qual
-echo ">>>>>Running abi-load..."
-abi-load -r meta/SRR7032226_run.xml -e meta/SRR7032226_experiment.xml -o SRR7032226
-rm -r SRR7032226 SRR7032226_F3*
+# echo ">>>>>Running abi-load..."
+# abi-load -r meta/SRR7032226_run.xml -e meta/SRR7032226_experiment.xml -o SRR7032226
+rm -rf SRR7032226 SRR7032226_F3*
 
 echo ">>>>>Running sam-dump..."
 sam-dump --output-file SRR6650398.sam SRR6650398
@@ -67,14 +67,14 @@ rm -r SRR6650398 SRR6650398.sam
 
 echo ">>>>>Running illumina-dump..."
 illumina-dump --qseq 1 SRR6650398
-echo ">>>>>Running illumina-load..."
-illumina-load -r meta/SRR6650398_illumina_run.xml -e meta/SRR6650398_experiment.xml -o SRR6650398
-rm -r SRR6650398 SRR6650398_0_0001_qseq.txt
+# echo ">>>>>Running illumina-load..."
+# illumina-load -r meta/SRR6650398_illumina_run.xml -e meta/SRR6650398_experiment.xml -o SRR6650398
+rm -rf SRR6650398 SRR6650398_0_0001_qseq.txt
 
 echo ">>>>>Running sff-dump..."
 sff-dump SRR2042184
-echo ">>>>>Running sff-load..."
-sff-load -r meta/SRR2042184_run.xml -e meta/SRR2042184_experiment.xml -o SRR2042184
+# echo ">>>>>Running sff-load..."
+# sff-load -r meta/SRR2042184_run.xml -e meta/SRR2042184_experiment.xml -o SRR2042184
 
 echo ">>>>>Running vdb-dump..."
 vdb-dump -f tab -C READ SRR2042184 | awk '{print ">" "SRR2042184." NR "\n" $0}' > SRR2042184.fasta



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/63cf3ac188e9e2157270764a1350af3296c324bb...4acc0f4f33ac4766b969f89b46a91307874faa67

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/63cf3ac188e9e2157270764a1350af3296c324bb...4acc0f4f33ac4766b969f89b46a91307874faa67
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