The terminal output and log file to support the issue at [bcbio/bcbio-nextgen#885]
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bcbio_nextgen vep installation bug (terminal output)
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| 2015-06-11 14:53:37 +0200 | |
| export FTP_PASSIVE=1 && /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl -a a -d /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib -c /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/share/data | |
| Using non-default installation directory /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib - you will probably need to add /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib to your PERL5LIB | |
| Setting up directories | |
| Downloading required files | |
| - fetching ensembl | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| ^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations: | |
| CAfile: /etc/pki/tls/certs/ca-bundle.crt | |
| CApath: none | |
| - unpacking /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip | |
| format error: file is too short | |
| at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 683. | |
| Archive::Zip::Archive::_findEndOfCentralDirectory('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 597 | |
| Archive::Zip::Archive::readFromFileHandle('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 565 | |
| Archive::Zip::Archive::read('Archive::Zip::Archive=HASH(0x281ee30)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 1154 | |
| Archive::Extract::_unzip_az('Archive::Extract=HASH(0x1a6fa60)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 432 | |
| Archive::Extract::extract('Archive::Extract=HASH(0x1a6fa60)', 'to', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990 | |
| main::unpack_arch('/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 292 | |
| main::install_api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 133 | |
| main::api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 101 | |
| Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip' at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip] | |
| End-of-central-directory signature not found. Either this file is not | |
| a zipfile, or it constitutes one disk of a multi-part archive. In the | |
| latter case the central directory and zipfile comment will be found on | |
| the last disk(s) of this archive. | |
| zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or | |
| /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period. | |
| at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip' | |
| Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip] | |
| End-of-central-directory signature not found. Either this file is not | |
| a zipfile, or it constitutes one disk of a multi-part archive. In the | |
| latter case the central directory and zipfile comment will be found on | |
| the last disk(s) of this archive. | |
| zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or | |
| /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period. | |
| Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| HOMEBREW_VERSION: 0.9.5 | |
| ORIGIN: https://github.com/Homebrew/linuxbrew.git | |
| HEAD: d0844607d93192f6012cf19676c157cbfc31954d | |
| Last commit: 20 hours ago | |
| HOMEBREW_PREFIX: /home/mpschr/bin/bcbionextgen/tools | |
| HOMEBREW_CELLAR: /home/mpschr/bin/bcbionextgen/tools/Cellar | |
| CPU: 24-core 64-bit 6 | |
| OS X: 0-x86_64 | |
| Xcode: N/A | |
| CLT: N/A | |
| Clang: N/A | |
| X11: N/A | |
| System Ruby: 1.9.3-p484 => /usr/bin/ruby1.9.1 | |
| Perl: /usr/bin/perl | |
| Python: /home/mpschr/anaconda3/bin/python => /home/mpschr/anaconda3/bin/python3.4 | |
| Ruby: /usr/bin/ruby => /usr/bin/ruby1.9.1 | |
| Java: 1.8.0_45 | |
| CC: /usr/bin/gcc => /usr/bin/gcc-4.8 | |
| CXX: /usr/bin/g++ => /usr/bin/g++-4.8 | |
| CFLAGS: -Os -w -pipe | |
| CXXFLAGS: -Os -w -pipe | |
| CPPFLAGS: -isystem/home/mpschr/bin/bcbionextgen/tools/include | |
| LDFLAGS: -L/home/mpschr/bin/bcbionextgen/tools/lib -Wl,-rpath,/home/mpschr/bin/bcbionextgen/tools/lib | |
| MAKEFLAGS: -j24 | |
| CMAKE_PREFIX_PATH: /home/mpschr/bin/bcbionextgen/tools | |
| PKG_CONFIG_LIBDIR: /home/mpschr/bin/bcbionextgen/tools/lib/pkgconfig:/usr/lib/pkgconfig | |
| PATH: /home/mpschr/bin/bcbionextgen/tools/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin/bcbionextgen/tools/Library/ENV/scm |
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| ==> Installing vep from chapmanb/homebrew-cbl | |
| ==> Downloading https://github.com/Ensembl/ensembl-tools/archive/4a86cbf.zip | |
| Already downloaded: /home/mpschr/.cache/Homebrew/vep-79_2015-04-13.zip | |
| ==> Verifying vep-79_2015-04-13.zip checksum | |
| unzip /home/mpschr/.cache/Homebrew/vep-79_2015-04-13.zip | |
| Archive: /home/mpschr/.cache/Homebrew/vep-79_2015-04-13.zip | |
| 4a86cbf5b2229cef36dda20492f7678cdbd0f466 | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/.travis.yml | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/ | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/AssemblyMapper.pl | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/README.txt | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/assemblymapper.in | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/IDmapper.pl | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/README.txt | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/idmapper.in | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/region_reporter/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/region_reporter/README.txt | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/region_reporter/region_report.pl | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/INSTALL.pl | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/README.txt | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/convert_cache.pl | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/example_GRCh37.vcf | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/example_GRCh38.vcf | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/filter_vep.pl | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/gtf2vep.pl | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/convert_cache.t | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/filter_vep.t | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/test.conf | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/TestPlugin.pm | |
| extracting: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/filter.list | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/filter.txt | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/filter.vcf | |
| extracting: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/test_vep_input.txt.gz | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/variant_effect_predictor.t | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/variant_effect_predictor.pl | |
| creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/travisci/ | |
| inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/travisci/harness.sh | |
| ==> export FTP_PASSIVE=1 && /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl -a a -d /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib -c /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/share/data | |
| Using non-default installation directory /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib - you will probably need to add /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib to your PERL5LIB | |
| Setting up directories | |
| Downloading required files | |
| - fetching ensembl | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| ^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations: | |
| CAfile: /etc/pki/tls/certs/ca-bundle.crt | |
| CApath: none | |
| - unpacking /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip | |
| format error: file is too short | |
| at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 683. | |
| Archive::Zip::Archive::_findEndOfCentralDirectory('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 597 | |
| Archive::Zip::Archive::readFromFileHandle('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 565 | |
| Archive::Zip::Archive::read('Archive::Zip::Archive=HASH(0x281ee30)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 1154 | |
| Archive::Extract::_unzip_az('Archive::Extract=HASH(0x1a6fa60)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 432 | |
| Archive::Extract::extract('Archive::Extract=HASH(0x1a6fa60)', 'to', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990 | |
| main::unpack_arch('/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 292 | |
| main::install_api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 133 | |
| main::api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 101 | |
| Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip' at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip] | |
| End-of-central-directory signature not found. Either this file is not | |
| a zipfile, or it constitutes one disk of a multi-part archive. In the | |
| latter case the central directory and zipfile comment will be found on | |
| the last disk(s) of this archive. | |
| zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or | |
| /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period. | |
| at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip' | |
| Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip] | |
| End-of-central-directory signature not found. Either this file is not | |
| a zipfile, or it constitutes one disk of a multi-part archive. In the | |
| latter case the central directory and zipfile comment will be found on | |
| the last disk(s) of this archive. | |
| zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or | |
| /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period. | |
| Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990. | |
| ==> Formula | |
| Tap: chapmanb/homebrew-cbl | |
| Path: /home/mpschr/bin/bcbionextgen/tools/Library/Taps/chapmanb/homebrew-cbl/vep.rb | |
| ==> Configuration | |
| HOMEBREW_VERSION: 0.9.5 | |
| ORIGIN: https://github.com/Homebrew/linuxbrew.git | |
| HEAD: d0844607d93192f6012cf19676c157cbfc31954d | |
| Last commit: 20 hours ago | |
| HOMEBREW_PREFIX: /home/mpschr/bin/bcbionextgen/tools | |
| HOMEBREW_CELLAR: /home/mpschr/bin/bcbionextgen/tools/Cellar | |
| CPU: 24-core 64-bit 6 | |
| OS X: 0-x86_64 | |
| Xcode: N/A | |
| CLT: N/A | |
| Clang: N/A | |
| X11: N/A | |
| System Ruby: 1.9.3-p484 => /usr/bin/ruby1.9.1 | |
| Perl: /usr/bin/perl | |
| Python: /home/mpschr/anaconda3/bin/python => /home/mpschr/anaconda3/bin/python3.4 | |
| Ruby: /usr/bin/ruby => /usr/bin/ruby1.9.1 | |
| Java: 1.8.0_45 | |
| ==> ENV | |
| CC: /usr/bin/gcc => /usr/bin/gcc-4.8 | |
| CXX: /usr/bin/g++ => /usr/bin/g++-4.8 | |
| CFLAGS: -Os -w -pipe | |
| CXXFLAGS: -Os -w -pipe | |
| CPPFLAGS: -isystem/home/mpschr/bin/bcbionextgen/tools/include | |
| LDFLAGS: -L/home/mpschr/bin/bcbionextgen/tools/lib -Wl,-rpath,/home/mpschr/bin/bcbionextgen/tools/lib | |
| MAKEFLAGS: -j24 | |
| CMAKE_PREFIX_PATH: /home/mpschr/bin/bcbionextgen/tools | |
| PKG_CONFIG_LIBDIR: /home/mpschr/bin/bcbionextgen/tools/lib/pkgconfig:/usr/lib/pkgconfig | |
| PATH: /home/mpschr/bin/bcbionextgen/tools/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin/bcbionextgen/tools/Library/ENV/scm |
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