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* Add a package for Trimmomatic
See the discussion about installing jar files in #4386.
Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place.
* Fix bad format statement
Apparently something like this "blah{}".format(...) works (it's missing
something inside the curly braces) but fails the travis test.
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The two given versions of mariadb are not fetchable under the given
URL, probably because older versions are purged and only kept in
an archive.
Add two working, latest revisions of each release line.
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For @:6, java is included in languages=all and requires zip.
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Somehow the path to `CMakeLists.txt` via the class property
`root_cmakelists_dir` was relative but is now actually relative
to `spack-build/`.
Close 4324 by providing a path relative to the source repo
of the stage via a method instead of a member variable
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* Package: libharu (PDF)
C++ PDF generation library, necessary for wt
* Package: WT
Adds `wt` "witty", a Qt-like C++ web framework for GUIs
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* Add package for vcftools@0.1.14
The package munges the various perl scripts so that their sbang lines
point to the depended upon perl (perhaps with Spack sbanger in the
dance) instead of relying on `/usr/bin/env perl`.
As it stands it installs its Perl libraries into `prefix/lib` and then
depends on `setup_environment` to prepend that dir onto PERL5LIB.
See my [vcftools issue
80](https://github.com/vcftools/vcftools/issues/80) for a discussion
about fixing its non-functional attempt at isolating itself from
PERL5LIB shenanigans.
* perl dependency should be build/run
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xmlto migrated to https://pagure.io/xmlto
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fetch libaio via the debian mirrors, the same way as archlinux builds
it (from original, unmodified sources):
https://git.archlinux.org/svntogit/packages.git/commit/trunk/PKGBUILD?h=packages/libaio&id=a8ec32dd3988668809e6c6affe678db04db3fc76
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* Ensure Config.pm has correct setting for cc
Run a filter after install so that Config.pm records the compiler that
Spack built the package with. If this isn't done, $Config{cc} will be
set to Spack's cc wrapper script.
* Also patch compilers Config_heavy.pl
This patch sets ld=gcc, which appears to work. I'm not sure if
there's a good way to get at the ld that Spack uses.
* Clean up quoting
* Fix pattern for Config.pm
Does not start at beginning of line...
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What the user wants, the user etc....
Add info for STAR@2.4.2a. It's URL looks different, so added a URL for
it. This broke the URL for the current version, so added a URL for it
also (known bug).
*Minimally* tested on CentOS 7.
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*Minimally* tested on CentOS 7.
Stole the `install_target` bit from zip....
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* python: ensure that distutils sets valid compiler options for RPATH on cray
* python: add cray-rpath patches for python@2.3:3.0.1 and python@3.1:
* python: in patch(..., when="@a:b platform=c"), limit b must be specified
* python: assume that python@4 will break the cray patches
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* petsc: add 3.7.6
* slepc: add 3.7.4
* hypre: remove whitespace
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* added STAR aligner package
* fixed flake errors
* PATH NOW WORKS
* STAR install now works
* star install now perfected
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* Added pgi support for suite-sparse package
* Patch modified
* added 'CFOPENMP={0}'.format(self.compiler.openmp_flag) for -mp flag
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* Fix mummerplot when ^perl@5.20:
Calling defined() on a hash has been deprecated for ages. It became
an error in perl@5.20. If we're building with a perl where it's
illegal, we should fix it.
* Simplify call to filter_file
Treat the first arg to filter_file as a string rather than
a regex, so that we don't have to figure out the escapes.
* Patch mummerplot for *any* perl version.
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* Fix bwa url's
Work around varying github URLs.
See #4365 for details.
* Restore main url entry
@adamjstewart pointed out that the package still needs a main url
so that `spack versions` works.
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* Add --configure-args/vars support to RPackage
* Docstring formatting change
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- Add a `spack gpg` subcommand in anticipation of signed binaries.
- GPG keys are stored in var/spack/gpg, and the spack gpg command manages them.
- Docs are included on the command.
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* Add info for jdk@7u80 (not downloadable)
Add version info for jdk@7u80. Oracle does't seem to be
distributing it any longer so there's no reasonable URL to
provide, but for those of us who already have the tarball
this is useful.
* Flake8 cleanup
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* added libdrm 2.4.75 per #4316
* removed 'list_url'
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* Add info for fastqc@0.11.4
* Delete the bamutil package (included by mistake)
The bamutil package was included by mistake, the commit deletes it.
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* updating mfem version
* changing mfem tarball extension to .tar.gz
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Specify either "--with-scalapack-dir" or "--with-scalapack-lib --with-scalapack-include". But not both!
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* Added pgi support for superlu-dist package
* added self.compiler.pic_flag
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* Add mpi support to R
* Add multiple precision math routines to R
* Updated the URL to match the version
* Remove duplicate packages
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* Correct Build type
* r-adegenet and dependent packages
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* Touch up string expansion.
I'm chasing this:
```
$ (module purge; spack install perl %gcc/5.4.0)
==> Error: No installed spec matches the hash: '%s'
```
There's something deeper going on, but the error message isn't helpful.
After this change it tells me this:
```
$ (module purge; spack install perl %gcc/5.4.0)
==> Error: No installed spec matches the hash: '5.4.0'
```
Which is weird because `5.4.0` is not a hash... Whatever is going on here, the error message needs to be fixed.
* Flake8 whitespace
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* trilinos: add DTK external package
* Making +dtk and ~tpetra conflict
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* fix parser
* Removed xfails
* cleaned up debug print statements
* make use of these changes in gcc
* Added comment explaining unreachable line, line left for added protection
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