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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Missing pigx-common file in source installation #183

Closed AnjaCaRa closed 2 years ago

AnjaCaRa commented 2 years ago

When running ./bootstrap.sh in the course of pigx_bsseq source installation the following error occurs:

./bootstrap.sh ./bootstrap.sh autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I pigx-common/common/m4 aclocal: warning: couldn't open directory 'pigx-common/common/m4': No such file or directory autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: running: /gnu/store/c0fl0g4kn9s6kb142l6dj18sqm53ya4j-autoconf-2.71/bin/autoconf --force configure.ac:32: error: possibly undefined macro: AC_MSG_ERROR If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. autoreconf: error: /gnu/store/c0fl0g4kn9s6kb142l6dj18sqm53ya4j-autoconf-2.71/bin/autoconf failed with exit status: 1

The missing file can be fetch from a set of scripts common to all pigx-pipelines by using git submodule update --init

rekado commented 2 years ago

Yes, you need to fetch all code, including the common submodule.