Adds recipe for mccortex #10860
Adds recipe for mccortex #10860
Conversation
winni2k
commented
Sep 7, 2018
winni2k
commented
- I have read the guidelines for bioconda recipes.
- This PR adds a new recipe.
- AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
- This PR updates an existing recipe.
- This PR does something else (explain below).
|
@bioconda/core: I think this PR is ready to merge. |
| - {{ compiler('cxx') }} | ||
| host: | ||
| - autoconf | ||
| - automake |
There was a problem hiding this comment.
Build tools go into build:, so autoconf and automake can go there. Do you even need them?
There was a problem hiding this comment.
Will do, but see comment below.
|
|
||
| export CFLAGS="-I$PREFIX/include" | ||
| export LDFLAGS="-L$PREFIX/lib" | ||
| export CPATH=${PREFIX}/include |
There was a problem hiding this comment.
Just optics, but write CPATH="$PREFIX/include" for readability
There was a problem hiding this comment.
Sure! But someone should probably fix the docs where I copied this from: https://bioconda.github.io/troubleshooting.html#zlib-errors
There was a problem hiding this comment.
Agreed. See bioconda/bioconda.github.io#22
| for make_file in libs/string_buffer/Makefile $(find libs/seq_file -name Makefile) $(find libs/seq-align -name Makefile) Makefile; do | ||
| sed -i.bak 's/-lz/-lz $(LDFLAGS)/' $make_file | ||
| done | ||
|
|
There was a problem hiding this comment.
Think you could make a PR upstream and reference it here? No need to delay the package, but feeding these things upstream would be nice.
There was a problem hiding this comment.
Wait ... if this tool uses autoconf/autotools, why do you need to patch the Makefiles?
There was a problem hiding this comment.
Mccortex has extensive dependencies that are all part of the source code release. The patching is applied to only a small number of all the make files in the mccortex source code. I need autoreconf for other make files...
There was a problem hiding this comment.
Happy to fix the other issues in an upstream PR.
|
Thanks @winni2k |
* Add mccortex * Refactor meta.yaml * Refactor meta.yaml * Add libtool build dependency * Maybe autoconf is the right library * Fix build number * Also need automake * fix sed issue in Mac OS X * Remove unneeded LIBRARY_PATH in build.sh * Fix minor comments from #10860 * bumb build number
