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Update blast to 2.9.0 #15550

Merged
merged 12 commits into from
May 24, 2019
Merged

Update blast to 2.9.0 #15550

merged 12 commits into from
May 24, 2019

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dpryan79
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@dpryan79 dpryan79 commented May 23, 2019 •
edited

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

@dpryan79
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This is another attempt at #14620. Ping @pmenzel since you asked about this (it's likely to fail at first at least).

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biocondabot bot commented May 23, 2019 •
edited

Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
linux-64 blast-2.9.0-h20b68b9_0.tar.bz2 repodata.json
osx-64 blast-2.9.0-h58d6d27_0.tar.bz2 repodata.json

You may alsu use conda to install these:

  • For packages in linux-64: 
    conda install -c https://58700-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
  • For packages in osx-64: 
    conda install -c https://58703-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
blast 2.9.0--h20b68b9_0
showcurl "https://58700-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/blast%3A2.9.0--h20b68b9_0.tar.gz" | gzip -dc | docker load

@eggzilla
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@dpryan79 thanks for giving that a try, I will try to help :-)

@dpryan79
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Thanks @eggzilla!

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dpryan79 commented May 23, 2019 •
edited

ar is currently being given a wrong parameter somehow while making libblast_unit_test_util.a

@dpryan79
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Altenatively, it errors on libncbi_xreader.a. Either way, it's handling $AR incorrectly.

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Works on Linux at least.

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dpryan79 commented May 24, 2019 •
edited

At the moment I've switched this from using gnutls to openssl. In the meta.yaml something is mentioned about remote queries then not working, which is obviously a problem. That needs to be fixed before merging.

@dpryan79
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This is a trove of useful information: #6073

@npavlovikj npavlovikj mentioned this pull request May 24, 2019
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@dpryan79
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gnutls is now being used again on both Linux and OSX. It builds for me locally on OSX, we'll see if Linux works still.

@dpryan79
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Fingers crossed, I've gotten this to at least compile and pass (non-mulled) testing with gnutls on both linux and OSX.

@dpryan79
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OMG it compiled! @eggzilla Can you give this a whirl and see if the -remote option works? It'd be best if that were tested before merging.

@dpryan79
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@bioconda-bot merge

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biocondabot bot commented May 24, 2019 •
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Upload & Merge started. Reload page to view progress.

  • Checks OK
  • Fetching 2 packages and 1 images
  • Uploaded image biocontainers/blast:2.9.0--h20b68b9_0
  • Uploaded package linux-64/blast-2.9.0-h20b68b9_0.tar.bz2
  • Uploaded package osx-64/blast-2.9.0-h58d6d27_0.tar.bz2
  • Creating squash merge

@biocondabot biocondabot bot merged commit 730f5ea into master May 24, 2019
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biocondabot bot commented May 24, 2019

@dpryan79, your request to merge succeeded: Pull Request successfully merged

@dpryan79 dpryan79 deleted the blast_it_all branch May 24, 2019 18:42
epruesse added a commit to epruesse/bioconda-recipes that referenced this pull request May 25, 2019
@epruesse
Merge branch 'master' into colinbrislawn-patch-2
d8eda61 
* master: (336 commits)
  Rebuild libgtextutils (bioconda#14659)
  set minced=0.3 (bioconda#15575)
  Update to plantcv v3.3.0 (bioconda#15539)
  add cami-opal recipe (bioconda#15573)
  Tango (bioconda#15570)
  stacks: bump version 2.4 (bioconda#15546)
  Bump segtools build for newer python versions (bioconda#15572)
  Update blast to 2.9.0 (bioconda#15550)
  add fastqsplitter recipe (bioconda#15568)
  Update xopen (bioconda#15566)
  r-probmetab - fix conda getting stuck on solving environment (bioconda#15519)
  Change sha256 for PGCGAP (bioconda#15565)
  Update PGCGAP to v1.0.2 (bioconda#15562)
  pb-falcon-0.3.3 (bioconda#15559)
  Spoa (bioconda#15555)
  seqbuster: bump to latest version (bioconda#15558)
  update irida uploader 0.2.1 (bioconda#15557)
  Super distance (bioconda#15551)
  Fix nanoplotter (bioconda#15548)
  Pycoqc requires h5py (bioconda#15545)
  ...
kpalin pushed a commit to kpalin/bioconda-recipes that referenced this pull request Aug 7, 2019
@dpryan79 @kpalin
Update blast to 2.9.0 (bioconda#15550)
ecef0d6 
Package uploads complete: [ci skip]
 - biocontainers/blast:2.9.0--h20b68b9_0
 - linux-64/blast-2.9.0-h20b68b9_0.tar.bz2
 - osx-64/blast-2.9.0-h58d6d27_0.tar.bz2
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@dpryan79 @eggzilla