This is a repository to support a fork of blasr code, renamed to blasrmc for name conflict. It is immediately legacy.

[mchaisso]

new file:   blasr-mc/build.sh
new file:   blasr-mc/meta.yaml

ℹ️
Bioconda has finished the GCC7 migration. If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. Bioconda utils - update-pinning will assist you with that. If you have any questions please use issue 13578.

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• [ x] I have read the guidelines for bioconda recipes.
• [ x] This PR adds a new recipe.
• [ x] 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).

[mchaisso]

@bioconda/core when this finishes bioconda-test, can this PR be reviewed? It is my first bioconda PR.

[bgruening]

@mchaisso if this package is not meant to be used and obsolete maybe a private channel would be better than bioconda?

[bgruening]

not needed, imho

[bgruening]

start with 0

[bgruening]

can you add a comment why this pinning is needed?

[bgruening]

Can you also add why this fork is needed and what are the special features?

[bgruening]

the binary is called blasrmc without a dash, is this correct?

[bgruening]

here you use c++98 but below c++11

[bgruening]

https://github.com/mchaisso/blasr your link does not work.

[mchaisso]

It's to support the phased-sv software which still uses this code -- it just isn't used for day to day read mapping any more, so that comment was a bit of hyperbole. I can still put it in a separate phased-sv channel if need be. -Mark

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On Sun, Apr 14, 2019 at 7:44 AM Björn Grüning ***@***.***> wrote: ***@***.**** commented on this pull request. @mchaisso <https://github.com/mchaisso> if this package is not meant to be used and obsolete maybe a private channel would be better than bioconda? ------------------------------ In recipes/blasr-mc/meta.yaml <#14445 (comment)> : > + name: blasr-mc + version: "1.MC.rc47.3" + +source: + url: https://github.com/mchaisso/blasr/archive/1.MC.rc47.3.tar.gz + md5: c2a3a1a4083ca0355c1603fb1fb3be15 + +build: + number: 1 + +requirements: + build: + - {{ compiler('cxx') }} + host: + - hdf5 <1.8.19x + - libstdcxx-ng not needed, imho ------------------------------ In recipes/blasr-mc/meta.yaml <#14445 (comment)> : > @@ -0,0 +1,32 @@ +package: + name: blasr-mc + version: "1.MC.rc47.3" + +source: + url: https://github.com/mchaisso/blasr/archive/1.MC.rc47.3.tar.gz + md5: c2a3a1a4083ca0355c1603fb1fb3be15 + +build: + number: 1 start with 0 ------------------------------ In recipes/blasr-mc/meta.yaml <#14445 (comment)> : > +source: + url: https://github.com/mchaisso/blasr/archive/1.MC.rc47.3.tar.gz + md5: c2a3a1a4083ca0355c1603fb1fb3be15 + +build: + number: 1 + +requirements: + build: + - {{ compiler('cxx') }} + host: + - hdf5 <1.8.19x + - libstdcxx-ng + + run: + - hdf5 <1.8.19x can you add a comment why this pinning is needed? ------------------------------ In recipes/blasr-mc/meta.yaml <#14445 (comment)> : > + - hdf5 <1.8.19x + - libstdcxx-ng + + run: + - hdf5 <1.8.19x + - libstdcxx-ng + +test: + commands: + - blasrmc -h + + +about: + home: https://github.com/mchaisson/blasr + license: GNU General Public License v3 (GPLv3) + summary: 'This is a fork of the original PacBio blasr, renamed blasrmc to avoid naming conflicts.' Can you also add why this fork is needed and what are the special features? ------------------------------ In recipes/blasr-mc/meta.yaml <#14445 (comment)> : > @@ -0,0 +1,32 @@ +package: + name: blasr-mc the binary is called blasrmc without a dash, is this correct? ------------------------------ In recipes/blasr-mc/build.sh <#14445 (comment)> : > @@ -0,0 +1,14 @@ +#!/usr/bin/env bash + +export PKG_CONFIG_LIBDIR="${PREFIX}"/lib/pkgconfig + +# HDF5 doesn't have pkgconfig files yet +export CPPFLAGS="-isystem ${PREFIX}/include " +export CPPOPTS="-std=c++98" here you use c++98 but below c++11 ------------------------------ In recipes/blasr-mc/meta.yaml <#14445 (comment)> : > + - {{ compiler('cxx') }} + host: + - hdf5 <1.8.19x + - libstdcxx-ng + + run: + - hdf5 <1.8.19x + - libstdcxx-ng + +test: + commands: + - blasrmc -h + + +about: + home: https://github.com/mchaisson/blasr https://github.com/mchaisso/blasr your link does not work. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#14445 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABTzPlrZm0VHJU94Yql6pOtXKP4mx8L6ks5vgz7RgaJpZM4crPHq> .

[daler]

Closing due to inactivity, please re-open if needed.