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Package Details: sra-tools 3.1.1-1
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Git Clone URL: | https://aur.archlinux.org/sra-tools.git (read-only, click to copy) |
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Package Base: | sra-tools |
Description: | A collection of tools and libraries for using data in the INSDC Sequence Read Archives |
Upstream URL: | https://github.com/ncbi/sra-tools |
Keywords: | insdc ncbi |
Licenses: | custom: public domain |
Provides: | ncbi-vdb |
Submitter: | apolih |
Maintainer: | kbipinkumar (BioArchLinuxBot) |
Last Packager: | BioArchLinuxBot |
Votes: | 3 |
Popularity: | 0.000000 |
First Submitted: | 2016-01-29 22:50 (UTC) |
Last Updated: | 2024-05-22 06:13 (UTC) |
Dependencies (10)
- gcc-libs (gcc-libs-gitAUR, gccrs-libs-gitAUR, gcc11-libsAUR, gcc-libs-snapshotAUR)
- glibc (glibc-gitAUR, glibc-linux4AUR, glibc-eacAUR, glibc-eac-binAUR, glibc-eac-rocoAUR)
- python (python37AUR, python311AUR, python310AUR)
- cmake (cmake-gitAUR) (make)
- doxygen (doxygen-gitAUR) (make)
- hdf5 (hdf5-gitAUR, hdf5-openmpi) (make)
- java-runtime (jre10AUR, jre12AUR, server-jreAUR, jdk10AUR, jdk10-openj9-binAUR, jdk7AUR, jre7AUR, amazon-corretto-16AUR, jdk8-graalvm-binAUR, jdk16-graalvm-binAUR, jdk16-adoptopenjdkAUR, jdk8-armAUR, liberica-jre-11-binAUR, jdk11-j9-binAUR, jre11-jbr-xdgAUR, jre16-openjdkAUR, jre14-openjdkAUR, amazon-corretto-18AUR, jre15AUR, jre14AUR, jre13AUR, jre16AUR, jre18-openjdkAUR, jdk-android-studioAUR, amazon-corretto-19-binAUR, jdk19-graalvm-binAUR, liberica-jre-11-full-binAUR, jdk19-graalvm-ee-binAUR, jdk13-openjdk-binAUR, liberica-jre-8-full-binAUR, jdk11-graalvm-binAUR, jre-openj9AUR, jdk11-graalvm-ee-binAUR, jre12-openjdkAUR, jdk11-dragonwell-standard-binAUR, jdk11-jetbrains-binAUR, jdk20-graalvm-binAUR, jdk17-graalvm-binAUR, jdk8-graalvm-ee-binAUR, amazon-corretto-20-binAUR, zulu-15-binAUR, jdk20-openj9-binAUR, zulu-13-binAUR, jdk8-dragonwell-extended-binAUR, jdk8-dragonwell-standard-binAUR, jdk11-dragonwell-extended-binAUR, jdk17-dragonwell-standard-binAUR, jre11AUR, jdk8-j9-binAUR, jdk7-j9-binAUR, jdk7r1-j9-binAUR, jdk8-dragonwell-extendedAUR, jre13-openjdkAUR, jre15-openjdkAUR, jdk21-graalvm-binAUR, jdk8AUR, jre8AUR, jdk-openj9-binAUR, jdk11-openj9-binAUR, jre17-jetbrainsAUR, jdk8-openj9-binAUR, jre-ltsAUR, jre17AUR, microsoft-openjdk-11-binAUR, microsoft-openjdk-17-binAUR, microsoft-openjdk-21-binAUR, jdk17-openj9-binAUR, liberica-nik-24-full-binAUR, jre21-jetbrains-gitAUR, jdk21-jetbrains-gitAUR, zulu-jre-fx-binAUR, amazon-corretto-17AUR, amazon-corretto-21-binAUR, amazon-corretto-22-binAUR, amazon-corretto-8AUR, amazon-corretto-11AUR, jdk-temurinAUR, jdk21-temurinAUR, jdk17-temurinAUR, jdk11-temurinAUR, zulu-21-binAUR, zulu-17-binAUR, zulu-11-binAUR, zulu-8-binAUR, liberica-jdk-8-full-binAUR, liberica-jdk-21-full-binAUR, jdk8-temurinAUR, mandrel-binAUR, mandrel24-binAUR, zulu-17-fx-binAUR, liberica-jdk-17-full-binAUR, liberica-jdk-11-lite-binAUR, liberica-jdk-11-full-binAUR, liberica-jdk-11-binAUR, jdk17-graalvm-ee-binAUR, jdk21-graalvm-ee-binAUR, jdk22-graalvm-ee-binAUR, jdk20-graalvm-ee-binAUR, jdk8-perfAUR, jdk22-graalvm-binAUR, jre19-openjdkAUR, zulu8-fx-binAUR, zulu11-fx-binAUR, zulu17-fx-binAUR, zulu21-fx-binAUR, jdk21-jetbrains-binAUR, jre-jetbrainsAUR, jre-openjdk-wakefieldAUR, jdk-openjdk-wakefieldAUR, jdk17-jetbrains-binAUR, zulu-jdk-fx-binAUR, java-openjdk-binAUR, liberica-jdk-full-binAUR, jre21-jetbrainsAUR, jdk17-zulu-prime-binAUR, jdk21-openj9-binAUR, jre17-zulu-binAUR, jreAUR, jdkAUR, jre21-zulu-binAUR, java-openjdk-ea-binAUR, zing-21-binAUR, zing-8-binAUR, jdk23-graalvm-ee-binAUR, jdk-openjdk, jdk11-openjdk, jdk17-openjdk, jdk21-openjdk, jre-openjdk, jre11-openjdk, jre17-openjdk, jre21-openjdk, jre8-openjdk) (make)
- libxml2 (libxml2-gitAUR, libxml2-2.9AUR) (make)
- mbedtls (mbedtls-gitAUR, mbedtls-dtlsAUR) (make)
- python-ngsAUR (optional) – python module for ncbi sra-tools
Latest Comments
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kbipinkumar commented on 2023-09-20 09:49 (UTC) (edited on 2023-09-20 09:50 (UTC) by kbipinkumar)
@luka5 @leuko thanks for your suggestions. the updated PKGBUILDS builds packages just fine on our project's, BioArchlinux, build server. it would be better if you use Bioarchlinux repo for installing packages. AUR serves as backup to push updated PKGBUILDS whenever a package is successfully built.
luka5 commented on 2023-06-28 09:25 (UTC)
@leuko coreutils changed the behavor of
mv -n
also known asmv --no-clobber
in v9.2 from silently doing nothing to failing. In v9.3 they introduced--update=none
which works as-n
before. The NEWs says:To achieve the same behavior as before, one would need to change
-n
to--update=none
.leuko commented on 2023-04-24 13:25 (UTC)
Error during building of
sra-tools
(the second part ofbuild()
):This is addressed in https://github.com/ncbi/sra-tools/pull/772/files and can be fixed (until the next release) using:
There is another error in
package()
:The lines that remove the unnecessary suffixes seems to error out. I fixed them using:
pdimens commented on 2019-07-05 13:27 (UTC)
Error: Failed to commit transaction: failed retrieving file 'perl-file-copy-recursive-0.44-2-any.pkg.tar.xz' from ct.mirror.garr.it : Connection timed out after 30000 milliseconds
Galaxy commented on 2019-05-29 07:35 (UTC)
'/usr/bin/kget -> kget.2' is conflicted with Extra/kget at <https://www.archlinux.org/packages/extra/x86_64/kget/>.
Would you rename the one in sra-tools ?
mollitz commented on 2018-12-19 15:27 (UTC)
pkgbuild fails because the installer is not capable of accessing https:
Running 43 test cases...
*** No errors detected ++++++++++++++++++++++++++++++++++++++++++++++++++++++ Run /tmp/trizen-moritz/ncbi-vdb/src/build_dir/ncbi-vdb/linux/gcc/x86_64/rel/test-bin/test-ngs_sra Running 67 test cases... 2018-12-19T15:20:16 test-ngs_sra.1.0.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2018-12-19T15:20:16 test-ngs_sra.1.0.0 int: file not open while identifying file within network system module - cannot KSocketGetRemoteEndpoint 2018-12-19T15:20:16 test-ngs_sra.1.0.0 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing unknown IP from '10.5.117.40' 2018-12-19T15:20:16 test-ngs_sra.1.0.0 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '10.5.117.40' 2018-12-19T15:20:16 test-ngs_sra.1.0.0 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/000000/SRR000001' /tmp/trizen-moritz/ncbi-vdb/src/ncbi-vdb-2.9.3/test/ngs/ngstest_sra.cpp(97): last checkpoint before exception "NGS_ReadCollectionMake(SRR000001) failed" ...
pwl commented on 2016-11-18 08:27 (UTC)
apolih commented on 2016-11-17 17:30 (UTC)
apolih commented on 2016-11-17 17:25 (UTC)
pwl commented on 2016-11-17 15:08 (UTC)
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