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tetomonti / Hydra

A flexible RNASeq pipeline
Apache License 2.0
4 stars 1 forks source link

Move conda package making into the repository #9

Closed gusef closed 9 years ago

tetomonti commented 9 years ago

Hi @yannpaul just moved all the relevant conda packages into the repository and now I'm trying to build them. This works well for some of the packages, but not so well for others. readline, python and samtools for example work without a glitch, while R-3.1.1 and bowtie2.2.2 do not. I get the following error::

conda build -c $CONDA_BLD_PATH bowtie2/2.2.2 Removing old build directory Removing old work directory BUILD START: bowtie2-2.2.2-monti Fetching package metadata: ......Error: Could not find Binstar user

Any ideas? Google was not very helpful. I have a montilab user on binstar, I tried logging into it and that did not make a difference. Also I tried it with the anaconda/2.2.0 version as well as with the ./dev_env version in montilab-p/projects/pipeline_dev/dev_env

Thank you!

gusef commented 9 years ago

Nevermind. If I just not specify the channel it seems to work just fine.

yannpaul commented 9 years ago

FYI the old file organization is all messed up. It works but it's ugly. I'm busy now but can try to take a look tomorrow. On Thu, May 7, 2015 at 4:39 PM gusef notifications@github.com wrote:

Nevermind. If I just not specify the channel it seems to work just fine.

— Reply to this email directly or view it on GitHub https://github.com/montilab/Hydra/issues/9#issuecomment-100012083.

gusef commented 9 years ago

Thanks. So far I copied only the packages that we actually need, which cleans it up, but I just remembered you told me conda can automatically build all required packages if there are recipes and the directories are named correctly. Going to look into that!

yannpaul commented 9 years ago

If you want to work on it then you need to rename the directories from package/version to package-version. Then conda build hydra-2.0.0 will look relative to that dir for all missing dependencies. On Thu, May 7, 2015 at 4:47 PM gusef notifications@github.com wrote:

Thanks. So far I copied only the packages that we actually need, which cleans it up, but I just remembered you told me conda can automatically build all required packages if there are recipes and the directories are named correctly. Going to look into that!

— Reply to this email directly or view it on GitHub https://github.com/montilab/Hydra/issues/9#issuecomment-100013935.

gusef commented 9 years ago

finished, installation was tested by two different users