Package Details: sra-tools 3.1.1-1

Git Clone URL: https://aur.archlinux.org/sra-tools.git (read-only, click to copy)
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)

Required by (0)

Sources (2)

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 as mv --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:

** New features

  cp and mv now support --update=none to always skip existing files
  in the destination, while not affecting the exit status.
  This is equivalent to the --no-clobber behavior from before v9.2.

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 of build()):

...
/bin/sh: line 1: cd: /home/u/.cache/pikaur/build/sra-tools/src/sra-tools-3.0.3/build1/obj/ngs/ngs-java/javadoc/ngs-doc: No such file or directory

This is addressed in https://github.com/ncbi/sra-tools/pull/772/files and can be fixed (until the next release) using:

prepare(){
  ...
  sed -i 's|NGS_JAVADOC_DIR ${TARGDIR}/obj|NGS_JAVADOC_DIR ${TARGDIR}|g' ngs/ngs-java/CMakeLists.txt
}

There is another error in package():

mv: not replacing '....cache/pikaur/build/sra-tools/pkg/sra-tools/usr/bin/abi-dump'

The lines that remove the unnecessary suffixes seems to error out. I fixed them using:

  # Fix filenames: remove $pkgver suffix from end of binaries
  for filename in "$pkgdir"/usr/bin/*$pkgver; do
    mv $filename ${filename%.$pkgver}
  done

  # Fix filenames: remove -orig suffix from end of binaries
  for filename in "$pkgdir"/usr/bin/*-orig; do
    mv $filename ${filename%-orig}
  done

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, thanks for making this a package. This seems to be a very intricate piece of software indeed. I saw a lot of errors concerning https when running the tests, I'm afraid this might be the reason for the build failing.

apolih commented on 2016-11-17 17:30 (UTC)

Thanks for the feedback. That looks like a Python2/Python3 error to me. Probably it was running Python 3 but the authors expect Python 2. I can see if I can patch this.

apolih commented on 2016-11-17 17:25 (UTC)

Yes, I can add python-virtualenv. I'm not familiar enough with the software to know if the HTTPS changes are causing the issue. Actually navigating the build system is a challenge in itself. Thanks for your patch and comments.

pwl commented on 2016-11-17 15:08 (UTC)

From the upstream repository: "We have released new tools with version 2.8.0 that are HTTPS compatible and M-15-13 compliant as of October 7, 2016. Please be certain to update all of your binaries and configuration files." could this be the issue? This package is in version 2.7.0, which is outdated according to the above quote.

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