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heathsc / bs_call

DNA methylation and variant Caller for Bisulfite Sequencing Data.
GNU General Public License v3.0
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Add bs_call to bioconda #1

Closed karl616 closed 6 years ago

karl616 commented 6 years ago

Hi, I want to add bs_call to bioconda and have set up a recipe based on v2.0.1:

https://github.com/karl616/bioconda-recipes/commit/8b2c4968c71f1c440e95db63022d6e84a6943ff5

As a courtesy, before I merge it in, I wanted to ask if there are objections against this? Personally, I would find it practical to have access to bs_call through conda.

karl616 commented 6 years ago

Doing this, I have problem with openmp for macos. Is this something that is known?

heathsc commented 6 years ago

No objections at all.

Simon

On 17 Jul 2018, at 09:22, Karl Nordström notifications@github.com wrote:

Hi, I want to add bs_call to bioconda and have set up a recipe based on v2.0.1:

karl616/bioconda-recipes@8b2c496 https://github.com/karl616/bioconda-recipes/commit/8b2c4968c71f1c440e95db63022d6e84a6943ff5 As a courtesy, before I merge it in, I wanted to ask if there are objections against this? Personally, I would find it practical to have access to bs_call through conda.

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heathsc commented 6 years ago

It can be disabled - it has little to no effect. The configure script should do this automatically.

Simon

On 20 Jul 2018, at 14:13, Karl Nordström notifications@github.com wrote:

Doing this, I have problem with openmp for macos. Is this something that is known?

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karl616 commented 6 years ago

OK, then my problem is that I went ahead with the release version (v2.0.1). I didn't get the configure script to work there. Would it be possible to have a newer release? Ultimately based on the latest commit, the one that is linked from gemBS. That is my final target...

karl616 commented 6 years ago

(The reason the configure script of v2.0.1 fails is a missing Makefile.mk.in)

heathsc commented 6 years ago

Odd - I get src/Makefile.mk.in and GEMTools/Makefile.mk.in. There shouldn’t be any difference between the bs_call version in gemBS and the ‘standalone’ version.

Simon

On 20 Jul 2018, at 14:22, Karl Nordström notifications@github.com wrote:

(The reason the configure script of v2.0.1 fails is a missing Makefile.mk.in)

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karl616 commented 6 years ago

That is true. But for bioconda I must work with releases: https://github.com/heathsc/bs_call/releases

and in the commit tagged v2.0.1 src/Makefile.mk.in is missing.

It was fixed here: https://github.com/heathsc/bs_call/commit/03dfcf9d4854f3b163a1b5c657f617779e68ceaf

heathsc commented 6 years ago

OK, I have made a new release - v2.0.2

On 20 Jul 2018, at 15:58, Karl Nordström notifications@github.com wrote:

That is true. But for bioconda I must work with releases: https://github.com/heathsc/bs_call/releases https://github.com/heathsc/bs_call/releases and in the commit tagged v2.0.1 src/Makefile.mk.in is missing.

It was fixed here: 03dfcf9 https://github.com/heathsc/bs_call/commit/03dfcf9d4854f3b163a1b5c657f617779e68ceaf — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/heathsc/bs_call/issues/1#issuecomment-406626635, or mute the thread https://github.com/notifications/unsubscribe-auth/ADHPd1uoEB3ZiLJCBpCXvC88yrxja3APks5uIfACgaJpZM4VSZJf.

karl616 commented 6 years ago

Thanks!

On Sat, Jul 21, 2018 at 11:37 AM Simon Heath notifications@github.com wrote:

OK, I have made a new release - v2.0.2

On 20 Jul 2018, at 15:58, Karl Nordström notifications@github.com wrote:

That is true. But for bioconda I must work with releases: https://github.com/heathsc/bs_call/releases < https://github.com/heathsc/bs_call/releases> and in the commit tagged v2.0.1 src/Makefile.mk.in is missing.

It was fixed here: 03dfcf9 < https://github.com/heathsc/bs_call/commit/03dfcf9d4854f3b163a1b5c657f617779e68ceaf

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karl616 commented 6 years ago

I have merged in the bs_call recipe into bioconda. It worked better with the updated version but I ended up forcibly disabling openmp for macos as I was unable to get it working otherwise. Anyhow, bs_call is now present in bioconda and with the repository active it can be installed with: conda install bs_call I'll close this issue.