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2016-08-06Call configure `--with-libpcre=...` to use our pcreGeorge Hartzell1-1/+1
An earlier commit claimed that this package depends_on('pcre') but I didn't fix the call to configure that enabled it. This fixes that.
2016-08-06Enable depends_on('pcre') alsoGeorge Hartzell1-3/+1
While I have the patient on the operating table, @adamjstewart asked me to uncomment and test the depends_on('pcre'). Did it and it Works For Me(tm).
2016-08-06Add depends_on('perl') to git packageGeorge Hartzell1-3/+3
This commit changes the git package to depend_on('perl'). The system perl is not always sufficient to install git (e.g. a CentOS7 system with the development tools group installed has perl but not the ExtUtils::MakeMaker package that git needs) and one can't always update the system's perl. This PR depends_on PR #1339, which adds a perl package to spack.
2016-08-06Switch to using *std_cmake_argsGeorge Hartzell4-7/+4
2016-08-06Flake8 whitespace cleanupGeorge Hartzell4-4/+8
2016-08-06Add Bio++ tool suite and supporting libsGeorge Hartzell4-0/+173
Add the Bio++ suite and its supporting libraries.
2016-08-06Add package for mafftGeorge Hartzell1-0/+42
2016-08-06Add package for exonerateGeorge Hartzell1-0/+44
2016-08-06Fix name of bpp-suite (missing -...)George Hartzell1-1/+1
2016-08-06Add package for prankGeorge Hartzell1-0/+44
2016-08-06opium: add new packageDenis Davydov1-0/+55
2016-08-05Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkitbecker332-0/+83
Add package for fastx toolkit
2016-08-05Merge pull request #1452 from hartzell/feature/add-package-for-samtoolsbecker334-29/+101
Add package for samtools
2016-08-05Remove lingering FIXME commentaryGeorge Hartzell1-3/+0
2016-08-05Samtools depends on htslib from 1.3.1 onwardGeorge Hartzell1-2/+2
Samtools used to (before 1.3.1) include it's own copy of htslib. Going forward, it needs to use the standalone htslib.
2016-08-05Merge pull request #1460 from glennpj/fix_list_vcsbecker331-8/+12
Catch error for version in VCS
2016-08-05Merge pull request #1453 from hartzell/feature/add-package-for-seqtkbecker331-0/+43
Add package for seqtk
2016-08-05Merge pull request #1450 from hartzell/feature/add-package-for-bwabecker331-0/+52
Add package for bwa
2016-08-05Catch error for version in VCSGlenn Johnson1-8/+12
This PR will catch the error where the url can not be determined from a VCS URL, such as git. It will print a message to the console and move on because it should not be a fatal error at this point in the process. This should fix #1459.
2016-08-05Merge pull request #1442 from suraia/update-scorep-2.0becker333-21/+39
Update Score-P to 2.0 Most likely this can be generalized to link against older versions of dependencies, but it looks good for now.
2016-08-04Flake8 cleanupGeorge Hartzell1-4/+5
2016-08-04Add Trilinos 12.6.4 (#1447)Bruno Turcksin1-0/+1
2016-08-04Add package for seqtkGeorge Hartzell1-0/+43
Seqtk is a tool for working with fast[aq] files.
2016-08-04Add package for bcftoolsGeorge Hartzell1-0/+43
2016-08-04Update samtools to support v1.3.1George Hartzell2-29/+16
Update the samtools package to support v1.3.1, which - now uses configure script; and - now depends on external htslib package. The dependency on mpc seems to have been bogus, it's never linked in, nor is it mentioned in the source tree. I *do* have a version in /usr/lib64, but ldd does not sure it being linked in either.... By depending on 'ncurses' I can do away with the need for the patch.
2016-08-04Add package for htslibGeorge Hartzell1-0/+41
Htslib was pulled out of samtools and made into a standalone thing. This commit adds a packag for it, in support of the samtools package.
2016-08-04Add package for fastx toolkitGeorge Hartzell1-0/+43
Tools for working with FASTA/FASTQ files.
2016-08-04Add package for libgtextutilsGeorge Hartzell1-0/+43
Gordon's Text utils Library, in support of fastx toolkit.
2016-08-04Make flake8 happy (long lines)George Hartzell1-0/+52
2016-08-04sbang filtering now works on non-writable files. (#1445)Todd Gamblin2-3/+26
- sbang now changes mode to writable and restores mode if a file is not writable.
2016-08-04flake8 fixesMichael Kuhn3-20/+27
2016-08-04Merge pull request #1330 from suraia/fix-ascii-graphbecker333-121/+101
Fix graph command with ASCII output
2016-08-04Merge pull request #1437 from jgalarowicz/update-xercescbecker331-4/+5
Update the version of xerces-c, where the developers remove the old v…
2016-08-04Merge pull request #1438 from jgalarowicz/update-libmonitorbecker331-5/+3
Update libmonitor to use its new github location, it does not exist w…
2016-08-04Merge pull request #1444 from tobbez/fix_indent_spiderbecker331-14/+14
Fix incorrect indentation in spack.util.web._spider
2016-08-04Merge pull request #1443 from davydden/pkg/dealii_pythonbecker331-2/+15
dealii: add optional python bindings
2016-08-04Merge pull request #1431 from hartzell/feature/add-package-for-unisonbecker332-0/+94
Add package for unison (and ocaml)
2016-08-04Fix flake8 issuesTorbjörn Lönnemark1-10/+10
2016-08-04dealii: add optional python bindingsDenis Davydov1-2/+15
2016-08-04Fix incorrect indentationTorbjörn Lönnemark1-5/+5
2016-08-04Update Score-P to 2.0Michael Kuhn3-1/+12
2016-08-04flake8 fixesMichael Kuhn2-103/+83
2016-08-04Fix tests.Michael Kuhn2-12/+11
2016-08-04Fix graph command with ASCII output.Michael Kuhn2-8/+9
2016-08-03Fix #1429: Remove git dep from gettext; break circular dependency.Todd Gamblin1-4/+0
- It's not really a circular dependency -- git is a run dependency of gettext - We can revert this change when Spack is smart enough to make git a run dependency and build it.
2016-08-03Fix flake8 errors for: Update libmonitor to use its new github location, it ↵Jim Galarowicz1-2/+1
does not exist where the package file now points to.
2016-08-03Fix flake8 errors for Update the version of xerces-c, where the developers ↵Jim Galarowicz1-2/+3
remove the old version, so there is no fallback.
2016-08-03Update libmonitor to use its new github location, it does not exist where ↵Jim Galarowicz1-3/+2
the package file now points to.
2016-08-03Update the version of xerces-c, where the developers remove the old version, ↵Jim Galarowicz1-2/+2
so there is no fallback.
2016-08-03Merge pull request #1433 from JRWynneIII/error_message_fixTodd Gamblin1-1/+1
Fix typo for error message when compiler doesn't exist for arch
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