add gffread #2
add gffread #2
Conversation
Signed-off-by: Pablo <[email protected]>
| locations and structure. GffRead and GffCompare are open source programs | ||
| that provide extensive and efficient solutions to manipulate files in a GTF | ||
| or GFF format. While GffRead can convert, sort, filter, transform, or | ||
| cluster genomic features, GffCompare can be used to compare and merge | ||
| different gene annotations.""" |
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The author created two different repos for gffread and gffcompare.
I think we should only talk about gffread inside this package.
| executables = ["gffread"] | ||
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| def install(self, spec, prefix): | ||
| make("../gclib") |
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I suspect this won't be accepted by the Spack folks, since this make line invokes a git clone of a separate repo
https://github.com/gpertea/gffread/blob/558c97f5b39b5801d9beaf752e46911814e97830/Makefile#L84-L85
We should instead package gclib into a separate recipe, and add it as a dependency of gffread. I'll work on that now.
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| def install(self, spec, prefix): | ||
| make("../gclib") | ||
| make("release") |
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https://github.com/gpertea/gffread/blob/558c97f5b39b5801d9beaf752e46911814e97830/Makefile#L84-L85
If I remember make correctly, calling make release could cause the ../gclib step of the makefile to be executed anyway, which we want to avoid (see comment above). I think we should use make gffread once the gclib package has been included and added as a dependency.
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I craeted the gclib package, which is a "collection" of headers that the author https://github.com/gpertea uses throughout different projects, and makes extending packaging to other programs easier (e.g. https://github.com/gpertea/gcompare). It's unclear to me how the two repos are related to each other, i.e. whether we can mix and match them, but I tried adding version 0.12.1 of both packages and asked spack to build them, but it failed, therefore I added a constraint so that 0.12.7 is only built with 0.12.7 (which are the only versions so far). |
…ck#37560) Co-authored-by: Harmen Stoppels <[email protected]>
Add gffread. This recipe is an adaptation of https://anaconda.org/bioconda/gffread