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spack/var/spack/repos/builtin/packages/augustus/package.py

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copyrights: update all files with license headers for 2021 - [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files - [x] update all licensed files to say 2013-2021 using `spack license update-copyright-year` - [x] appease mypy with some additions to package.py that needed for oneapi.py
2021-01-02 15:10:28 +08:00
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# Spack Project Developers. See the top-level COPYRIGHT file for details.
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
#
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
import glob
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
imports: sort imports everywhere in Spack (#24695) * fix remaining flake8 errors * imports: sort imports everywhere in Spack We enabled import order checking in #23947, but fixing things manually drives people crazy. This used `spack style --fix --all` from #24071 to automatically sort everything in Spack so PR submitters won't have to deal with it. This should go in after #24071, as it assumes we're using `isort`, not `flake8-import-order` to order things. `isort` seems to be more flexible and allows `llnl` mports to be in their own group before `spack` ones, so this seems like a good switch.
2021-07-09 06:12:30 +08:00
from spack import *
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
class Augustus(MakefilePackage):
"""AUGUSTUS is a program that predicts genes in eukaryotic
genomic sequences"""
start of work to add spack audit packages-https checker (#25670) This PR will add a new audit, specifically for spack package homepage urls (and eventually other kinds I suspect) to see if there is an http address that can be changed to https. Usage is as follows: ```bash $ spack audit packages-https <package> ``` And in list view: ```bash $ spack audit list generic: Generic checks relying on global variables configs: Sanity checks on compilers.yaml Sanity checks on packages.yaml packages: Sanity checks on specs used in directives packages-https: Sanity checks on https checks of package urls, etc. ``` I think it would be unwise to include with packages, because when run for all, since we do requests it takes a long time. I also like the idea of more well scoped checks - likely there will be other addresses for http/https within a package that we eventually check. For now, there are two error cases - one is when an https url is tried but there is some SSL error (or other error that means we cannot update to https): ```bash $ spack audit packages-https zoltan PKG-HTTPS-DIRECTIVES: 1 issue found 1. Error with attempting https for "zoltan": <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: Hostname mismatch, certificate is not valid for 'www.cs.sandia.gov'. (_ssl.c:1125)> ``` This is either not fixable, or could be fixed with a change to the url or (better) contacting the site owners to ask about some certificate or similar. The second case is when there is an http that needs to be https, which is a huge issue now, but hopefully not after this spack PR. ```bash $ spack audit packages-https xman Package "xman" uses http but has a valid https endpoint. ``` And then when a package is fixed: ```bash $ spack audit packages-https zlib PKG-HTTPS-DIRECTIVES: 0 issues found. ``` And that's mostly it. :) Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-02 14:46:27 +08:00
homepage = "https://bioinf.uni-greifswald.de/augustus/"
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz"
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
# Releases have moved to github
version('3.4.0', sha256='2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8')
augustus: fix bam2wig auxprog build (#10362) * augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-05 00:36:10 +08:00
version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
Update URL parsing regexes and tests (#13411) * Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
2019-10-29 09:27:54 +08:00
version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
augustus: fix bam2wig auxprog build (#10362) * augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-05 00:36:10 +08:00
url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
checksums: use sha256 checksums everywhere We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
2019-10-11 13:44:41 +08:00
version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee',
augustus: fix bam2wig auxprog build (#10362) * augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-05 00:36:10 +08:00
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz')
checksums: use sha256 checksums everywhere We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
2019-10-11 13:44:41 +08:00
version('3.2.3', sha256='a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514',
augustus: fix bam2wig auxprog build (#10362) * augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-05 00:36:10 +08:00
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
depends_on('perl', type=('build', 'run'))
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
depends_on('python', when='@3.3.1:', type=('build', 'run'))
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
depends_on('bamtools')
depends_on('gsl')
depends_on('boost')
depends_on('zlib')
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
depends_on('htslib')
depends_on('bcftools')
depends_on('samtools')
augustus: fix bam2wig auxprog build (#10362) * augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-05 00:36:10 +08:00
depends_on('curl', when='@3.3.1:')
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
depends_on('sqlite', when='@3.4.0:')
depends_on('mysql-client', when='@3.4.0:')
depends_on('mysqlpp', when='@3.4.0:')
depends_on('lp-solve', when='@3.4.0:')
depends_on('suite-sparse', when='@3.4.0:')
# Trying to use filter_file here got too complicated so use a patch with a
# corresponding environment variable
patch('bam2wig_Makefile.patch', when='@3.4.0:')
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
def edit(self, spec, prefix):
Fix replacement of embedded 'gcc' in augustus (#14116) PR #13975 added makefile filtering to replace gcc/g++ with the spack compiler. This conflicts with other filtering that is done in the package to add paths for dependencies. The text of the dependency paths might have 'gcc' in the path name, depending on the install_path_scheme, and that was being replaced by the new compiler filters. That would mangle the path to the dependecy resulting in a failed build. This PR moves the compiler filters to be before the other filters to make sure that the compiler is set before the dependency paths.
2019-12-12 10:19:27 +08:00
# Set compile commands for each compiler and
# Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1)
if self.version >= Version('3.3.1-tag1'):
with working_dir(join_path('auxprogs', 'utrrnaseq', 'Debug')):
filter_file('g++', spack_cxx, 'makefile', string=True)
filter_file('g++ -I/usr/include/boost', '{0} -I{1}'
.format(spack_cxx,
self.spec['boost'].prefix.include),
'src/subdir.mk', string=True)
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
# Makefiles to set spack compiler over gcc/g++
Fix replacement of embedded 'gcc' in augustus (#14116) PR #13975 added makefile filtering to replace gcc/g++ with the spack compiler. This conflicts with other filtering that is done in the package to add paths for dependencies. The text of the dependency paths might have 'gcc' in the path name, depending on the install_path_scheme, and that was being replaced by the new compiler filters. That would mangle the path to the dependecy resulting in a failed build. This PR moves the compiler filters to be before the other filters to make sure that the compiler is set before the dependency paths.
2019-12-12 10:19:27 +08:00
makefiles = [
'auxprogs/aln2wig/Makefile',
'auxprogs/bam2hints/Makefile',
'auxprogs/bam2wig/Makefile',
'auxprogs/compileSpliceCands/Makefile',
'auxprogs/homGeneMapping/src/Makefile',
'auxprogs/joingenes/Makefile',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'src/Makefile',
Fix replacement of embedded 'gcc' in augustus (#14116) PR #13975 added makefile filtering to replace gcc/g++ with the spack compiler. This conflicts with other filtering that is done in the package to add paths for dependencies. The text of the dependency paths might have 'gcc' in the path name, depending on the install_path_scheme, and that was being replaced by the new compiler filters. That would mangle the path to the dependecy resulting in a failed build. This PR moves the compiler filters to be before the other filters to make sure that the compiler is set before the dependency paths.
2019-12-12 10:19:27 +08:00
]
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
if self.version < Version('3.4.0'):
makefiles.append('auxprogs/checkTargetSortedness/Makefile')
if self.version >= Version('3.4.0'):
makefiles.extend([
'auxprogs/filterBam/src/Makefile',
'src/unittests/Makefile',
])
Fix replacement of embedded 'gcc' in augustus (#14116) PR #13975 added makefile filtering to replace gcc/g++ with the spack compiler. This conflicts with other filtering that is done in the package to add paths for dependencies. The text of the dependency paths might have 'gcc' in the path name, depending on the install_path_scheme, and that was being replaced by the new compiler filters. That would mangle the path to the dependecy resulting in a failed build. This PR moves the compiler filters to be before the other filters to make sure that the compiler is set before the dependency paths.
2019-12-12 10:19:27 +08:00
for makefile in makefiles:
filter_file('gcc', spack_cc, makefile, string=True)
filter_file('g++', spack_cxx, makefile, string=True)
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
bamtools = self.spec['bamtools'].prefix
bcftools = self.spec['bcftools'].prefix
htslib = self.spec['htslib'].prefix
samtools = self.spec['samtools'].prefix
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
with working_dir(join_path('auxprogs', 'filterBam', 'src')):
makefile = FileFilter('Makefile')
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = {0}'.format(bamtools))
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
makefile.filter('INCLUDES = *',
'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
Augustus hash (#7447) * augustus: 3.3 package hash changed * augustus: bamtools libraries now seem to be in lib64 * augustus: fix lib problem with older bamtools
2018-03-10 08:05:39 +08:00
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'LIBS = $(BAMTOOLS)/lib64'
Augustus hash (#7447) * augustus: 3.3 package hash changed * augustus: bamtools libraries now seem to be in lib64 * augustus: fix lib problem with older bamtools
2018-03-10 08:05:39 +08:00
'/libbamtools.a -lz')
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib/bamtools'
'/libbamtools.a -lz')
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
with working_dir(join_path('auxprogs', 'bam2hints')):
makefile = FileFilter('Makefile')
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
makefile.filter('/usr/include/bamtools',
'{0}/include/bamtools'.format(bamtools))
Augustus hash (#7447) * augustus: 3.3 package hash changed * augustus: bamtools libraries now seem to be in lib64 * augustus: fix lib problem with older bamtools
2018-03-10 08:05:39 +08:00
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'LIBS = {0}/lib64'
'/libbamtools.a -lz'.format(bamtools))
Augustus hash (#7447) * augustus: 3.3 package hash changed * augustus: bamtools libraries now seem to be in lib64 * augustus: fix lib problem with older bamtools
2018-03-10 08:05:39 +08:00
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'LIBS = {0}/lib/bamtools'
'/libbamtools.a -lz'.format(bamtools))
if self.version < Version('3.4.0'):
with working_dir(join_path('auxprogs', 'bam2wig')):
makefile = FileFilter('Makefile')
# point tools to spack installations
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
makefile.filter('BCFTOOLS=.*$',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'BCFTOOLS={0}/include'.format(bcftools))
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
makefile.filter('SAMTOOLS=.*$',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'SAMTOOLS={0}/include'.format(samtools))
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
makefile.filter('HTSLIB=.*$',
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
'HTSLIB={0}/include'.format(htslib))
# fix bad linking dirs
makefile.filter('$(SAMTOOLS)/libbam.a',
'$(SAMTOOLS)/../lib/libbam.a', string=True)
makefile.filter('$(HTSLIB)/libhts.a',
'$(HTSLIB)/../lib/libhts.a', string=True)
with working_dir(join_path('auxprogs', 'checkTargetSortedness')):
makefile = FileFilter('Makefile')
makefile.filter('SAMTOOLS.*=.*$',
'SAMTOOLS={0}/include'.format(samtools))
makefile.filter('LIBS=-lbam',
'LIBS=$(SAMTOOLS)/../lib/libbam.a',
string=True)
else:
mysql = self.spec['mysql-client'].prefix
mysqlpp = self.spec['mysqlpp'].prefix
lpsolve = self.spec['lp-solve'].prefix
augustus: fix bam2wig auxprog build (#10362) * augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-05 00:36:10 +08:00
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
with working_dir('src'):
makefile = FileFilter('Makefile')
makefile.filter(r'/usr/include/mysql\+\+',
'{0}/include/mysql++'.format(mysqlpp))
if '^mariadb-c-client' in spec:
makefile.filter('/usr/include/mysql',
'{0}/include/mariadb'.format(mysql))
else:
makefile.filter('/usr/include/mysql',
'{0}/include/mysql'.format(mysql))
makefile.filter('/usr/include/lpsolve',
'{0}/include/lpsolve'.format(lpsolve))
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
def install(self, spec, prefix):
install_tree('bin', join_path(self.spec.prefix, 'bin'))
install_tree('config', join_path(self.spec.prefix, 'config'))
install_tree('scripts', join_path(self.spec.prefix, 'scripts'))
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
@run_after('install')
def filter_sbang(self):
with working_dir(self.prefix.scripts):
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
pattern = '^#!.*'
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
repl = '#!{0}'.format(self.spec['perl'].command.path)
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
files = glob.glob("*.pl")
Fixes for augustus package - add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 02:21:21 +08:00
for file in files:
filter_file(pattern, repl, *files, backup=False)
augustus: add v3.4.0 and update package (#22879) - add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
2021-04-23 21:56:22 +08:00
repl = '#!{0}'.format(self.spec['python'].command.path)
files = glob.glob("*.py")
for file in files:
filter_file(pattern, repl, *files, backup=False)
def setup_build_environment(self, env):
if self.version >= Version('3.4.0'):
htslib = self.spec['htslib'].prefix
env.set('HTSLIBDIR', htslib)
Update URL parsing regexes and tests (#13411) * Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
2019-10-29 09:27:54 +08:00
def setup_run_environment(self, env):
env.set('AUGUSTUS_CONFIG_PATH', join_path(
New package augustus (#4586) * augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-23 05:00:43 +08:00
self.prefix, 'config'))
Update URL parsing regexes and tests (#13411) * Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
2019-10-29 09:27:54 +08:00
env.prepend_path('PATH', join_path(self.prefix, 'scripts'))
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