laninsky
commented
5 years ago Hi folks - the cluster staff rebuilt Augustus and it is now working. I still am not sure why the local installation didn't work, but in case it is handy I'm going to paste the easybuild eb file for the cluster-wide installation here for other people who may be having trouble (although I believe they built off the website rather than the bleeding edge repository):
easyblock = 'ConfigureMake'
(END)
name = 'AUGUSTUS'
version = '3.3.2'
homepage = 'http://bioinf.uni-greifswald.de/augustus/'
description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
toolchain = {'name': 'gimkl', 'version': '2017a'}
source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/']
sources = ['augustus-%(version)s.tar.gz']
patches = [
'%(name)s-3.3_bamtools_includepath.patch',
'%(name)s-3.3_no_symlinks_install.patch',
'%(name)s-3.3_SAMtools.patch',
]
#checksums = [
# 'b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee', # augustus-3.3.tar.gz
# 'cc48206918ca6fb75b55d3cd2870d6a139ba1ae10ea77e8c0d68eedd26142ddf', # AUGUSTUS-3.3_bamtools_includepath.patch
# 'afaa0136d8a0d7d060a5597384b88267e17c9b3cc9b60b0faebc6eff03f7bce1', # AUGUSTUS-3.3_no_symlinks_install.patch
#]
dependencies = [
('SAMtools', '1.8'),
('zlib', '1.2.11'),
('Boost', '1.61.0'),
('GSL', '2.3'),
('lp_solve', '5.5.2.5'),
('SuiteSparse', '4.5.4'),
('BamTools', '2.4.1'),
('SQLite', '3.16.2'),
]
skipsteps = ['configure']
prebuildopts = "make clean && "
buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX" CFLAGS="-std=c++11 -I$EBROOTSAMTOOLS/include/bam $CFLAGS -lpthread"'
installopts = 'INSTALLDIR=%(installdir)s'
sanity_check_paths = {
'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining',
'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes',
'bin/load2sqlitedb', 'bin/prepareAlign'],
'dirs': ['config', 'scripts'],
}
modextrapaths = {'PATH': 'scripts'}
modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
moduleclass = 'bio'
Hi folks,
Apologies if I've missed something dumb during installation here, but I'm a bit stuck. I'm running cat on a slurm system, but using a single machine just to try and minimise complications. I seem to be running into issues with my Augustus installation. It seems to get through the Augustus CGP step fine, but then fails with a SIGSEGV on the Augustus PB step. I originally posted this issue there (https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/118), but @ifiddes-10x suggested posting here.
Running the command outside of cat also gives an immediate Segmentation Fault. From previous issues I thought filename length could be an issue, so I copied out the offending files and renamed them (also attached here with the modified names), but still ran into the same issue running it outside of cat:
extrinsicCfgFile.tmp.txt hintsfile.tmp.txt input.tmp.txt
@ifiddes-10x had no trouble running augustus with these files so I strongly suspect this might have something to do with our cluster architecture (RedHat)/dependencies but I'm not savvy enough to track it down. I followed the instructions for compiling Augustus CGP in this repository ('''b8ce1b0'''), and I'm using modules for Samtools (1.8) and bedtools (2.26.0). I've tried using both the boost/zlib/samtools modules and installing both of these from scratch, but am still getting the same outcome. Any help would be really appreciated. I did a gdb traceback and got the following in case it helps track down the issue: