* Trailing whitespace cleanup
* Handcraft an install process for mummer (grumble)
Mummer punts on an installation step, they just build in and run from
the same directory.
Mummer also has various hardcoded paths built into it that allow it to
find other executables that it needs as well as its Perl library.
This updates the package to deal with this approach.
It patches the Makefile and scripts/Makefile so that the correct info
is fed to sed when it munges the perl scripts.
The install step is now finer grained and puts things where mummer
relatively wants to find them.
* Add perl dependency
* perl should be build/run dependency
* Fix whitespace
* Delete stray u at top of file
Two changes:
- It seems that Illumina version numbers are dotted and that the
dashed version in the 2.18... filename is an anomaly (based on the
names for 2.17.1.14 and 2.19.0). `url_for_version` does the right
thing for 2.18. It will need to be fixed when support for 2.19 is
added. 2.17 is no longer generally available so it gets a pass.
- Add version and hash for 2.17.1.14.
2.17.1.14 is no longer distributed. If you have a copy of the
source tarball, you can drop it into a local mirror w/ the name
mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
* Add mpi support to R
* Add multiple precision math routines to R
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* flex: create variant +lex that creates symlinks for lex and libl.{a,so}
* flex: enable variant +lex by default
* flex: use dso_suffix for portability; replace repetitive code with a loop
I need boost@1.54.0 for bcl2fastq2. I tested bcl2fastq2 using the
system compiler (gcc@4.8.5). My full build uses a spack-build
gcc@5.4.0.
boost@1.54.0 won't build. I found the answer
[here](https://github.com/hashdist/hashstack/issues/802) with the
details in [this upstream/boost
ticket](https://svn.boost.org/trac/boost/ticket/10125).
I've confirmed that these combo's build:
boost version| compiler
------------ | ------------------
boost@1.54.0 | gcc@4.8.5 (system)
boost@1.54.0 | gcc@5.4.0 (Spack)
boost@1.64.0 | gcc@5.5.0 (system)
* added openmpi support to meme
* openmpi is a link dependency which leverages r_path
* openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used
* added serial option and set mpi to not be default
* modified meme
* Add the gnupg package and missing dependencies. Update versions of existing dependencies.
* this ended up in the wrong repo
* put versions back, remove uneeded function
* OK ;)
* autopep8
* typo on npth line
* whitespace
* Add a new package for Open Babel
* Add post-installation tests, stolen from the fine folks at Homebrew
* Add patch to fix Python 3.6 support
* Add a more complete patch to get Python 3.6 support working
* Add patch to convert tabs to spaces in test script
testpdbformat.py contains mixed tabs and spaces
causing the unit tests to fail. With this patch,
all tests pass with flying colors.
* Add v1.1.26 and make crypto a variant
I need 1.1.26 for bcl2fastq2.
I also need to build it without crypto support.
* Initial support for bcl2fastq2
* Clean up commentary, messages, names
No substantial changes intended, just cleanup.
* fix flake8 and extra import
* The masked grammarian strikes again...
* Be normal (messages don't end in periods)
* When +crypto, add --with-crypto
Add `--with-crypto` to configure args when user hasn't explicitly set
`~crypto`.
* self.spec.satisfies is unsatisfying, in is in instead
See #4135, self.spec.satisfies has issues. @adamjstewart suggests
simply using in.
* Sphinx no longer supports Python 2.6
* Update vendored sphinxcontrib.programoutput from 0.9.0 to 0.10.0
* Documentation cannot be built in parallel
* Let Travis install programoutput for us
* Remove vendored sphinxcontrib-programoutput
Recent updates to the sphinx package prevent the vendored version
from being found in sys.path. We don't vendor sphinx, so it doesn't
make sense to vendor sphinxcontrib-programoutput either.
* added albacore package as well as dependency py-ont-fast5-api
* added py-cutadapt and dependency py-xopen
* made more changes to albacore and cutadapt as well as dependencies
* made changes again per @adamjstewart
* fixed by python n00b errors i think
* fixed?
* tw=79
* made changes to py-ont-fast5-api ont-albacore
* removed bad characters
* albacore requires setuptools as build and run dependency
* added vmd
* added back albacore
* removed vmd package
* added meme software
* libz is only needed as link depedency for meme
* added libxml2 libxslt libgcrypt as link dependencies
