biocore / conda-recipes Goto Github PK

The repo tagline reads

bioinformatic tools like blast+...

What version of blast would be useful?

• BLAST+: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
• legacy BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/

Would this repository be the right place to add a recipe for the program memsat-svm http://bioinfadmin.cs.ucl.ac.uk/downloads/memsat-svm/ that we are going to use for MicroProt?

https://github.com/biocore/biom-format

I know this would be covered in #3, but biom-format is a stand-alone project, it is being updated as part of QIIME 2, and I would find it immediately useful.

https://github.com/biocore/burrito
😄 🌯

Also needed for #56

I'm getting the following error in the deblur PR

Traceback (most recent call last):
  File "ci/main.py", line 9, in <module>
    from conda_build.config import config
ImportError: cannot import name 'config'

@Jorge-C , @RNAer any idea what is happening?

It's the default for tree-building, so I would like it.
It's under the GPLv2, as shown on the top of the source code:
http://www.microbesonline.org/fasttree/FastTree.c

Links here: http://www.microbesonline.org/fasttree/#Install

Ideally, we should only run the test the recipes that are changed in a pull request. building can take a long time, especially when large number of recipes are accumulated in the future.

When there are multiple builds on anaconda, the json you get from conda search is:

$ conda search --json --override-channels -c biocore --spec minced
{
  "minced": [
    {
      "arch": "x86_64", 
      "binstar": {
        "channel": "main", 
        "owner_id": "5621521bab59360b0dd04062", 
        "package_id": "562ee7589c73334dd79f873d"
      }, 
      "build": "0", 
      "build_number": 0, 
      "channel": "biocore", 
      "depends": [], 
      "extracted": true, 
      "features": [], 
      "fn": "minced-0.2.0-0.tar.bz2", 
      "full_channel": "https://conda.anaconda.org/t/ze-370af1ae-c3ae-439e-8821-1bfc65bfc225/biocore/osx-64/", 
      "installed": false, 
      "license": "GPL3", 
      "machine": "x86_64", 
      "md5": "9c226498c33a4b2d4463620be45e6b9c", 
      "name": "minced", 
      "operatingsystem": "darwin", 
      "platform": "osx", 
      "requires": [], 
      "size": 485165, 
      "subdir": "osx-64", 
      "target-triplet": "x86_64-any-darwin", 
      "type": null, 
      "version": "0.2.0"
    }, 
    {
      "arch": "x86_64", 
      "binstar": {
        "channel": "main", 
        "owner_id": "5621521bab59360b0dd04062", 
        "package_id": "562ee7589c73334dd79f873d"
      }, 
      "build": "1", 
      "build_number": 1, 
      "channel": "biocore", 
      "depends": [], 
      "extracted": false, 
      "features": [], 
      "fn": "minced-0.2.0-1.tar.bz2", 
      "full_channel": "https://conda.anaconda.org/t/ze-370af1ae-c3ae-439e-8821-1bfc65bfc225/biocore/osx-64/", 
      "installed": false, 
      "license": "GPL3", 
      "machine": "x86_64", 
      "md5": "dd157e7eaaf6c607740e471253bd4c19", 
      "name": "minced", 
      "operatingsystem": "darwin", 
      "platform": "osx", 
      "requires": [], 
      "size": 485339, 
      "subdir": "osx-64", 
      "target-triplet": "x86_64-any-darwin", 
      "type": null, 
      "version": "0.2.0"
    }
  ]
}

This will cause Travis to upload an existing build even the build number is not incremented. The offending line is this

This would be nice to have.

so that we can run it to build and upload locally as well if needed.

The future is arriving! And when it comes, it should be in a conda package. 🐍 📦

I'll take this one, and make sure it stays up and running throughout development. @gregcaporaso already got it building in travis.

Need to check muscle license...
Should ask Robert Edgar for permission too.

...or would that be an insane request? It'd be nice if anything to lower Travis deployment times

Useful for the EMP project and a useful alternative to vsearch and SortMeRNA.
https://github.com/torognes/swarm

Got this error when trying to install prodigal

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/mortonjt/Documents/micronota/micronota/bfillings/tests/test_prodigal.py", line 75, in test_predict_genes_wrong_input
    predict_genes(fp, self.temp_dir, 'foo')
AssertionError: "Sequence read failed \(file must be Fasta, Genbank, or EMBL format\)." does not match "Unacceptable application exit status: 1
Command:
cd "/home/mortonjt/Documents/micronota/micronota/bfillings/"; prodigal -d "/tmp/tmpei3o_9q3/foo.fna" -i "/home/mortonjt/Documents/micronota/micronota/bfillings/tests/data/empty" -o "/tmp/tmpei3o_9q3/foo.gbk" -a "/tmp/tmpei3o_9q3/foo.faa" > "/tmp/tmpFQMWrZcnRv8owY5dGdxd.txt" 2> "/tmp/tmpIUmEUFyqgxMcDOnPgbrt.txt"
StdOut:

StdErr:
prodigal: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by prodigal)

It'd be nice to have travis building every package as CI, and if successful uploading binaries to binstar.

Hi think the issue is that the check for presence of the package in the anaconda cloud exists with a status != 0 (because those new packages are not present) which then is interpreted picked up by the python calling function as an error (rather than an information) cause it to stop the program :-/

conda-recipes/ci/main.py function is_not_uploaded line 102

Hi,

I am currently writing the conda recipe for the RREfinder tool (https://github.com/Alexamk/RREFinder). This tool requires psipred (http://bioinf.cs.ucl.ac.uk/psipred/) for which you offer the conda recipe and the conda package via the biocore channel.

However, in bioconda, all dependencies must come from the following conda channels: defaults, conda-forge, bioconda. Therefore, I still miss the psipred dependency to build the RRefinder bioconda package: bioconda/bioconda-recipes#33650

I saw that you intended to migrate the psipred conda recipe to bioconda: #62 (comment)
Is this possible? That would be great and that would solve my dependency problem!

Tell me if I can help in any way!
I can open a new PR in bioconda with a recipe largely inspired by yours, if you want, but you are more legitimate than I am to do so :-)

Regards,

Loraine

It looks like qiime2 is not currently compatible with python 3.6

@RNAer @wasade maybe we should deactivate these tests for the time being?

There is some discussion of this in #61 (ping @wasade, as he brought this up there). I think we should investigate ending this project in favor of contributing to bioconda. Thoughts on this?

@jairideout did a little research into bioconda and found that they're funded by continuum, and have a bunch of the same packages that we have here, including QIIME and vsearch.

Looks like Travis fails whenever a new recipe is merged in, because the two different unix versions try to upload the same package at the same time with the result that one job fails and the other passes.
Can we do something about that?

It seems only ascii and - are allowed? What name should we use instead?

I am using blastlegacy for the new recipe "psipred". When I execute blastpgp it complains about missing BLOSSUM62 files. One need to point blast to the according file by setting the environment variable BLASTMAT to the correct dir.
Looks like this var is not set after installing blastlegacy via conda. Could someone else please doublecheck?!

OSX and linux are already taken care of, via travis-ci. We still need windows, probably via appveyor (see here).

Qiime currently uses fastq-join, which is part of ea-utils, for joining. So let's add it!
https://code.google.com/archive/p/ea-utils/downloads

VSEARCH now supports pairing and filtering, so qiime 2 could use vsearch for these functions, fully replacing fastq-join.

Not sure what's happening b/c if it was already present it shouldn't try building it either.

2015-11-05 03:05:26,938 INFO: Uploading: anaconda -t {token} upload -u {channel} {built}

Using anaconda-server api site https://api.anaconda.org

detecting package type ...

conda

extracting package attributes for upload ...

done

Uploading file biocore/minced/0.2.0/osx-64/minced-0.2.0-1.tar.bz2 ... 

Distribution already exists. Please use the -i/--interactive or --force options or `anaconda remove biocore/minced/0.2.0/osx-64/minced-0.2.0-1.tar.bz2`

[Conflict] (u'file osx-64/minced-0.2.0-1.tar.bz2 already exists for package minced version 0.2.0', 409)

Traceback (most recent call last):

  File "ci/main.py", line 133, in <module>

    build_upload_recipes(sys.argv[1], sys.argv[2])

  File "ci/main.py", line 50, in build_upload_recipes

    upload(name, version, channel)

  File "ci/main.py", line 129, in upload

    shell=True)

  File "/Users/travis/miniconda/lib/python2.7/subprocess.py", line 540, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'anaconda -t ze-b2e094e1-af48-4b13-a678-ac6f0e5e9581 upload -u biocore /Users/travis/miniconda/conda-bld/osx-64/minced-0.2.0-1.tar.bz2' returned non-zero exit status 1

The command "python ci/main.py recipes biocore" exited with 1.

provides a lot of useful functionality for processing illumina reads so may be useful