[med-svn] [Git][med-team/sra-sdk][master] 7 commits: debian/tests: Switch to modern encryption/decryption setup.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Tue Oct 26 00:59:59 BST 2021
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
7f0715fe by Aaron M. Ucko at 2021-10-25T18:21:07-04:00
debian/tests: Switch to modern encryption/decryption setup.
* run-unit-test: Replace protected repository configuration (no longer
supported as of ncbi-vdb 2.11.0) by --ngc [...].ngc.
* test-data.tar.gz: Replace dbGaP-0.enc_key by a copy of upstream's
test/prefetch/data/prj_phs710EA_test.ngc.
- - - - -
515157a8 by Aaron M. Ucko at 2021-10-25T18:22:59-04:00
sra-sdk changelog: Clarify that Andreas updated to 2.11.2.
- - - - -
0669b7fc by Aaron M. Ucko at 2021-10-25T18:27:24-04:00
debian/watch: Look for tags rather than releases.
GitHub currently lists none(!) of the latter.
- - - - -
99ea9619 by Aaron M. Ucko at 2021-10-25T18:27:56-04:00
routine-update: New upstream version
- - - - -
1309b538 by Aaron M. Ucko at 2021-10-25T18:27:58-04:00
New upstream version 2.11.3+dfsg
- - - - -
7c08db84 by Aaron M. Ucko at 2021-10-25T18:38:32-04:00
Merge tag 'upstream/2.11.3+dfsg'
Upstream version 2.11.3+dfsg
- - - - -
29f0375c by Aaron M. Ucko at 2021-10-25T18:40:06-04:00
routine-update: Ready to upload to unstable
- - - - -
10 changed files:
- CHANGES.md
- README.md
- build/Makefile.vers
- debian/changelog
- debian/tests/run-unit-test
- debian/tests/test-data/test-data.tar.gz
- debian/watch
- shared/toolkit.vers
- shared/toolkit.vers.h
- tools/driver-tool/imp_fasterq_dump.cpp
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,6 +1,12 @@
# NCBI External Developer Release:
+## SRA Toolkit 2.11.3
+**October 25, 2021**
+
+ **fasterq-dump, sratools**: fasta and fasta-unsorted parameters work correctly
+
+
## SRA Toolkit 2.11.2
**October 7, 2021**
=====================================
README.md
=====================================
@@ -15,14 +15,12 @@ using data in the INSDC Sequence Read Archives.
### ANNOUNCEMENT:
-October 7, 2021
-
-SRA data are now available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete more rapidly. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users that do not require full base quality scores for their analysis can request the SRA Lite version to save time on their data transfers. To request the SRA Lite data when using the SRA toolkit, set the "Prefer SRA Lite files with simplified base quality scores" option on the main page of the toolkit configuration- this will instruct the tools to preferentially use the SRA Lite format when available (please be sure to use toolkit version 2.11.2 or later to access this feature). The quality scores generated from SRA Lite files will be the same for each base within a given read (quality = 30 or 3, depending on whether the Read Filter flag is set to 'pass' or 'reject'). Data in the SRA Normalized Format with full base quality scores will continue to have a .sra file extension, while the SRA Lite files have a .sralite file extension. For more information please see our [data format](https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/) page.
-
+October 25, 2021. SRA Toolkit 2.11.3:
+fixed a bug in fasterq-dump: fasta and fasta-unsorted parameters work correctly.
+October 7, 2021. SRA Toolkit 2.11.2:
-
-October 7, 2021: SRA Toolkit 2.11.2.
+SRA data are now available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete more rapidly. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users that do not require full base quality scores for their analysis can request the SRA Lite version to save time on their data transfers. To request the SRA Lite data when using the SRA toolkit, set the "Prefer SRA Lite files with simplified base quality scores" option on the main page of the toolkit configuration- this will instruct the tools to preferentially use the SRA Lite format when available (please be sure to use toolkit version 2.11.2 or later to access this feature). The quality scores generated from SRA Lite files will be the same for each base within a given read (quality = 30 or 3, depending on whether the Read Filter flag is set to 'pass' or 'reject'). Data in the SRA Normalized Format with full base quality scores will continue to have a .sra file extension, while the SRA Lite files have a .sralite file extension. For more information please see our [data format](https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/) page.
August 17, 2021: SRA Toolkit 2.11.1.
=====================================
build/Makefile.vers
=====================================
@@ -23,4 +23,4 @@
# ===========================================================================
# SRA-TOOLS and library version
-VERSION = 2.11.2
+VERSION = 2.11.3
=====================================
debian/changelog
=====================================
@@ -1,8 +1,8 @@
-sra-sdk (2.11.2+dfsg-1) UNRELEASED; urgency=medium
+sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* Fix watchfile to detect new versions on github
- * New upstream version
+ * New upstream version 2.11.2.
* Standards-Version: 4.6.0 (routine-update)
* Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2)
* Skip test that test needs a *lot* of memory
@@ -17,8 +17,16 @@ sra-sdk (2.11.2+dfsg-1) UNRELEASED; urgency=medium
declarations within tools/driver-tool.
* d/p/run_unversioned_tools.patch (new): Look for tools by their
unversioned names, per Debian's simplified installation arrangement.
-
- -- Aaron M. Ucko <ucko at debian.org> Mon, 18 Oct 2021 21:34:57 -0400
+ * debian/tests: Switch to modern encryption/decryption setup.
+ - run-unit-test: Replace protected repository configuration (no longer
+ supported as of ncbi-vdb 2.11.0) by --ngc [...].ngc.
+ - test-data.tar.gz: Replace dbGaP-0.enc_key by a copy of upstream's
+ test/prefetch/data/prj_phs710EA_test.ngc.
+ * debian/watch: Look for tags rather than releases, as GitHub currently
+ lists none(!) of the latter.
+ * New upstream version 2.11.3.
+
+ -- Aaron M. Ucko <ucko at debian.org> Mon, 25 Oct 2021 18:29:10 -0400
sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium
=====================================
debian/tests/run-unit-test
=====================================
@@ -19,8 +19,6 @@ echo ">>>>>Running vdb-config..."
export VDB_CONFIG=$AUTOPKGTEST_TMP
export NCBI_SETTINGS=$AUTOPKGTEST_TMP/meta/u.mkfg
vdb-config --set repository/user/main/public/root=$AUTOPKGTEST_TMP/public
-vdb-config --set repository/user/protected/dbGaP-0/root=$AUTOPKGTEST_TMP/dbGaP-0
-vdb-config --set repository/user/protected/dbGaP-0/encryption-key-path=$AUTOPKGTEST_TMP/meta/dbGaP-0.enc_key
echo ">>>>>Running cache-mgr..."
cache-mgr --report
@@ -84,9 +82,9 @@ sra-pileup --function mismatch --minmismatch 10 -o stat.txt.gz --gzip SRR6650398
echo ">>>>>Running vdb-encrypt..."
cd dbGaP-0 # change directory to the project’s workplace
-vdb-encrypt ../SRR2042184.fasta ./
+vdb-encrypt --ngc ../meta/prj_phs710EA_test.ngc ../SRR2042184.fasta ./
echo ">>>>>Running vdb-decrypt..."
-vdb-decrypt SRR2042184.fasta.ncbi_enc
+vdb-decrypt --ngc ../meta/prj_phs710EA_test.ngc SRR2042184.fasta.ncbi_enc
cd ../
echo ">>>>>Running vdb-validate..."
=====================================
debian/tests/test-data/test-data.tar.gz
=====================================
Binary files a/debian/tests/test-data/test-data.tar.gz and b/debian/tests/test-data/test-data.tar.gz differ
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/ncbi/sra-tools/releases .*/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+ https://github.com/ncbi/sra-tools/tags .*/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
=====================================
shared/toolkit.vers
=====================================
@@ -1 +1 @@
-2.11.2
+2.11.3
=====================================
shared/toolkit.vers.h
=====================================
@@ -1 +1 @@
-#define TOOLKIT_VERS 0x020B0002
+#define TOOLKIT_VERS 0x020B0003
=====================================
tools/driver-tool/imp_fasterq_dump.cpp
=====================================
@@ -168,6 +168,8 @@ struct FasterqParams final : CmnOptAndAccessions
if ( strict ) ss << "strict" << std::endl;
if ( !bases.isEmpty() ) ss << "bases : " << bases << std::endl;
if ( append ) ss << "append" << std::endl;
+ if ( fasta ) ss << "fasta" << std::endl;
+ if ( fastaUnsorted ) ss << "fasta-unsorted" << std::endl;
return CmnOptAndAccessions::show(ss);
}
@@ -208,6 +210,8 @@ struct FasterqParams final : CmnOptAndAccessions
if ( strict ) builder . add_option( "--strict" );
if ( !bases.isEmpty() ) builder . add_option( "-B", bases );
if ( append ) builder . add_option( "-A" );
+ if ( fasta ) builder . add_option("--fasta");
+ if ( fastaUnsorted ) builder . add_option("--fasta-unsorted");
}
bool check() const override
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/e7f83da351870686b30ced879c48d1c7906c9604...29f0375c46231f15a6e24789232f4ddb548f83e2
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/e7f83da351870686b30ced879c48d1c7906c9604...29f0375c46231f15a6e24789232f4ddb548f83e2
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