Public bug reported: The sprai package contains a script "ezez_vx1.pl" which can be used to error correct genomic reads. The Perl script executes sophisticated shell pipelines of other tools; To fail early, each shell command starts with "set -o pipefail;" (line 265). However, as Ubuntu uses Dash as /bin/sh the script fails with an error "sh: 1: set: Illegal option -o pipefail".
Steps to reproduce: See [1] and the example files distributed with sprai. Possible solution: Patch the script to set $pipefail to "". I am no Perl monk, but I think a better way would be to make the Perl script run the command in bash. 1: http://zombie.cb.k.u-tokyo.ac.jp/sprai/Example.html Description: Ubuntu 18.04.2 LTS Release: 18.04 sprai: Installed: 0.9.9.23+dfsg-1 Candidate: 0.9.9.23+dfsg-1 Version table: *** 0.9.9.23+dfsg-1 500 500 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages 100 /var/lib/dpkg/status ProblemType: Bug DistroRelease: Ubuntu 18.04 Package: sprai 0.9.9.23+dfsg-1 [modified: usr/bin/ezez_vx1] ProcVersionSignature: Ubuntu 4.15.0-45.48-generic 4.15.18 Uname: Linux 4.15.0-45-generic x86_64 ApportVersion: 2.20.9-0ubuntu7.5 Architecture: amd64 CurrentDesktop: ubuntu:GNOME Date: Thu Feb 28 14:59:34 2019 DistributionChannelDescriptor: # This is a distribution channel descriptor # For more information see http://wiki.ubuntu.com/DistributionChannelDescriptor canonical-oem-somerville-xenial-amd64-20160624-2 InstallationDate: Installed on 2018-08-03 (208 days ago) InstallationMedia: Ubuntu 16.04 "Xenial" - Build amd64 LIVE Binary 20160624-10:47 SourcePackage: sprai UpgradeStatus: Upgraded to bionic on 2018-08-20 (191 days ago) ** Affects: sprai (Ubuntu) Importance: Undecided Status: New ** Tags: amd64 apport-bug bionic -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1818076 Title: sprai chokes on default shell To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/sprai/+bug/1818076/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
