Hi Kenneth. Thank you for your recommendation. Unfortunately the pandaseq installation failed. Here is a tail of log file.
Regards, Robert == 2017-03-23 10:38:23,849 easyblock.py:1346 INFO Using /sysapps/cluster/build/PANDAseq/2.11/foss-2016b/pandaseq-2.11/ as start dir == 2017-03-23 10:38:23,849 build_log.py:216 INFO configuring... == 2017-03-23 10:38:23,850 easyblock.py:2286 INFO Starting configure step == 2017-03-23 10:38:23,850 easyblock.py:2289 INFO Running method configure_step part of step configure == 2017-03-23 10:38:23,850 run.py:162 INFO running cmd: ./autogen.sh && ./configure --prefix=/sysapps/cluster/software/PANDAseq/2.11-foss-2016b == 2017-03-23 10:38:37,351 build_log.py:147 ERROR EasyBuild crashed with an error (at ?:124 in __init__): cmd "./autogen.sh && ./configure --prefix=/sysapps/cluster/software/PANDAseq/2.11-foss-2016b " exited with exitcode 77 and output: libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:17: installing './ar-lib' configure.ac:18: installing './compile' configure.ac:19: installing './config.guess' configure.ac:19: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' checking for a BSD-compatible install... /bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... no configure: error: in `/sysapps/cluster/build/PANDAseq/2.11/foss-2016b/pandaseq-2.11': configure: error: C compiler cannot create executables See `config.log' for more details (at easybuild/tools/run.py:449 in parse_cmd_output) == 2017-03-23 10:38:37,352 easyblock.py:2518 WARNING build failed (first 300 chars): cmd "./autogen.sh && ./configure --prefix=/sysapps/cluster/software/PANDAseq/2.11-foss-2016b " exited with exitcode 77 and output: libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4 == 2017-03-23 10:38:37,353 easyblock.py:276 INFO Closing log for application name PANDAseq version 2.11 From: <[email protected]> on behalf of Kenneth Hoste <[email protected]> Reply-To: "[email protected]" <[email protected]> Date: Thursday, March 23, 2017 at 10:28 AM To: "[email protected]" <[email protected]> Subject: Re: [easybuild] PANDAseq - static Hi Robert, On 23/03/2017 14:12, Klima, Robert (NIH/NIAID) [C] wrote: Hi, I am trying to install a static version of PANDAseq. I have modified pandaseq to use PANDAseq vers. 2.11 and toolchain foss-2016b. I have added: configopts = ['--enable-static=yes'] The installation was: COMPLETED: Installation ended successfully. However, I received the "error while loading shared libraries: libbz2.so.1.0". What other options should I use to create a static version? Maybe this this: toolchainopts = {'static': True} This will make EasyBuild include a -static in $CFLAGS and friends, which may be sufficient... regards, Kenneth Thank you, Robert ----- name = 'PANDAseq' version = '2.11' homepage = 'https://github.com/neufeld/pandaseq' description = """PANDAseq assembles Illumina Solexa overlapping pair-end reads.""" toolchain = {'name': 'foss', 'version': '2016b'} configopts = ['--enable-static=yes'] # source_urls = ['https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('libtool', '2.4.6'), ('bzip2', '1.0.6'), ('zlib', '1.2.8'), ] builddependencies = [('Autoconf', '2.69')] preconfigopts = "./autogen.sh &&" sanity_check_paths = { 'files': ['bin/pandaseq', 'bin/pandaseq-checkid', 'bin/pandaseq-hang', 'bin/pandaxs', 'lib/libpandaseq.%s' % SHLIB_EXT, 'lib/libpandaseq.a', 'lib/pkgconfig/pandaseq-%(version_major)s.pc'], 'dirs': ['include/pandaseq-%(version_major)s'], } moduleclass = 'bio'
