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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/sjackman/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.
Shaun Jackman sjackman @10xGenomics Vancouver, Canada https://sjackman.ca I am a computational biologist (PhD), a developer of Cell Ranger and Homebrew, an open-source programmer, an avid traveller, a singer, and an enthusiastic cook.

GFA-spec/GFA-spec 116

Graphical Fragment Assembly (GFA) Format Specification

10XGenomics/vartrix 72

Single-Cell Genotyping Tool

Linuxbrew/docker 48

🐳 🍺 🐧 Dockerfiles for running Homebrew on Linux on various distros

mozillascience/global-sprint-2016 35

repo for planning of Global Sprint 2016, June 2-3

jts/dbgfm 25

FM-index representation of a de Bruijn graph

10XGenomics/enclone 16

VDJ Clone Analysis Tools

Linuxbrew/homebrew-fonts 16

🖋 Formula of F🅾𝓝𝐓𝚂 (fork of Caskroom-fonts)

bcgsc/chromeqc 13

ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads

jennybc/stat540_2014 13

STAT540 Statistical Methods for High Dimensional Biology, January - April 2014

hackseq/modular-assembly-hs18 9

Mix and match modular genome assembler components

issue openedbrewsci/homebrew-bio

idba segmentation fault

  • [x] Confirmed this is a problem with brew installing one, specific formula and not every time you run brew? If it's a general brew problem please file this issue at https://github.com/Homebrew/brew/issues/new.
  • [x] Ran brew update and retried your prior step?
  • [x] Ran brew doctor, fixed all issues and retried your prior step?
  • [ ] Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
  • [x] If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?

The bottle doesn't work

I'm trying to use idba from the brewsci/bio tap, but I'm getting segmentation faults that seem to be rooted in compilation.

First, I tried the simple route:

$> brew install idba
==> Installing idba from brewsci/bio
==> Downloading https://archive.org/download/brewsci/bottles-bio/idba-1.1.3_2.sierra.bottle.tar.gz
Already downloaded: /Users/miguel/Library/Caches/Homebrew/downloads/8a78e6dc32c4ee9a1a50cd702c488248524826c3664352d1457f9af02de38d29--idba-1.1.3_2.sierra.bottle.tar.gz
==> Pouring idba-1.1.3_2.sierra.bottle.tar.gz
Warning: brewsci/bio/idba dependency gmp was built with a different C++ standard
library (libc++ from clang). This may cause problems at runtime.
🍺  /usr/local/Cellar/idba/1.1.3_2: 36 files, 5.8MB
$> idba_ud 
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/9/libgomp.1.dylib
  Referenced from: /usr/local/bin/idba_ud
  Reason: image not found
Abort trap: 6

Source installation doesn't work

Since I saw the warning about gmp, I tried the following:

  1. brew uninstall idba which worked fine
  2. brew reinstall -s gmp which seems to have worked fine as well (see log using -v)
  3. brew install idba, which produced the exact same output as above
  4. brew install -s idba, which generated the following output and never gave me back the prompt, so I had to kill it with Ctrl+C:
    ==> Installing idba from brewsci/bio
    ==> Downloading https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/hku-idba/lacto-genus.tar.gz
    Already downloaded: /Users/miguel/Library/Caches/Homebrew/downloads/0d76a9708baed3cf7d14e93853013aa81f9a77952c4387ea65054cf337aade6e--lacto-genus.tar.gz
    ==> Downloading https://github.com/loneknightpy/idba/archive/1.1.3.tar.gz
    Already downloaded: /Users/miguel/Library/Caches/Homebrew/downloads/03fd964aee8290422be93d479dc20a7126b0ff703747621a911bdd29808ae632--idba-1.1.3.tar.gz
    ==> aclocal
    ==> autoconf
    ==> automake --add-missing
    ==> ./configure --prefix=/usr/local/Cellar/idba/1.1.3_2
    ==> make
    ==> make check
    ^C
    One sec, cleaning up...
    
  5. In order to see what was the error, I did brew install -sv idba, which produced this log with tail:
    /Library/Developer/CommandLineTools/usr/bin/make  check-TESTS
    PASS: compact_sequence_unittest
    PASS: bit_edges_unittest
    PASS: kmer_unittest
    PASS: atomic_integer_unittest
    PASS: vertex_status_unittest
    ../test-driver: line 109: 97633 Segmentation fault: 11  "$@" > $log_file 2>&1
    FAIL: histgram_unittest
    ../test-driver: line 109: 97639 Segmentation fault: 11  "$@" > $log_file 2>&1
    FAIL: managed_list_unittest
    PASS: sequence_unittest
    PASS: short_sequence_unittest
    ^C
    One sec, cleaning up...
    
    
    As you can see, I also had to kill it with with Ctrl+C.
  6. Just to make sure, I also ran the tests for gmp, which seems to be fine:
    $> brew test -v gmp
    git config --replace-all homebrew.devcmdrun true
    ==> Installing 'bundler' gem
    ==> Testing gmp
    /usr/bin/sandbox-exec -f /private/tmp/homebrew20210307-92812-jwa4k0.sb ruby -W1 -- /usr/local/Homebrew/Library/Homebrew/test.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gmp.rb --verbose
    ==> /usr/bin/clang test.c -L/usr/local/Cellar/gmp/6.2.1/lib -lgmp -o test
    ==> ./test
    ==> /usr/bin/clang test.c /usr/local/Cellar/gmp/6.2.1/lib/libgmp.a -o test
    ==> ./test
    

gcc@9 doesn't work either

I saw that idba is listed in #1186, so I tried requiring gcc@9 by editing the formula locally to bump the revision and replace the gcc:

diff --git a/Formula/idba.rb b/Formula/idba.rb
index a90eabf..d39c964 100644
--- a/Formula/idba.rb
+++ b/Formula/idba.rb
@@ -4,7 +4,7 @@ class Idba < Formula
   homepage "https://i.cs.hku.hk/~alse/hkubrg/projects/idba/"
   url "https://github.com/loneknightpy/idba/archive/1.1.3.tar.gz"
   sha256 "6b1746a29884f4fa17b110d94d9ead677ab5557c084a93b16b6a043dbb148709"
-  revision 2
+  revision 3
   head "https://github.com/loneknightpy/idba.git"
 
   bottle do
@@ -16,7 +16,9 @@ class Idba < Formula
   depends_on "autoconf" => :build
   depends_on "automake" => :build
 
-  depends_on "gcc" if OS.mac? # needs openmp
+  on_macos do
+    depends_on "gcc@9" # needs openmp
+  end
 
   fails_with :clang # needs openmp
 

And reran brew install -sv idba but got the exact same result.

I'm fresh out of ideas here ☹️. Any help is greatly appreciated!

brew config

HOMEBREW_VERSION: 3.0.4-50-ga930e2b
ORIGIN: https://github.com/Homebrew/brew
HEAD: a930e2b36235d3c0b15f655752c76fadc35dc3fb
Last commit: 29 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: c5e98a5a9bbbbe4a635d293b47f44cac975e3863
Core tap last commit: 7 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: vi
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 2.6.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.3_2/bin/ruby
CPU: octa-core 64-bit icelake
Clang: 12.0 build 1200
Git: 2.24.3 => /Library/Developer/CommandLineTools/usr/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 10.15.7-x86_64
CLT: 12.4.0.0.1.1610135815
Xcode: N/A

created time in 4 hours

PR closed Linuxbrew/docker

Let a github action build all images

This excludes scratch and travis but can be easily extended. It also allows for an easy extension to upload all images to github afterwards

+29 -10

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SMillerDev

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created repositorybbehsaz/nrpminer_gnps

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PR opened brewsci/homebrew-bio

paml 4.9j
  • [ ] Have you followed the guidelines for contributing?
  • [ ] Have you checked that there aren't other open pull requests for the same formula update/change?
  • [ ] Have you built your formula locally with brew install --build-from-source FORMULA, where FORMULA is the name of the formula you're submitting?
  • [ ] Does your build pass brew audit --strict FORMULA (after doing brew install FORMULA)?

+3 -3

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push eventHomebrew/homebrew-linux-dev

Dawid Dziurla

commit sha cb22d2c12034be7be9eeb7f4105f6c37237a66dd

cmd: add not-migrated command (#193)

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PR merged Homebrew/homebrew-linux-dev

cmd: add not-migrated command

This command can in theory help us with all those migration stuff to homebrew-core of linux-specific changes.

It prints git diffs between homebrew-core/master and linuxbrew-core/master refs. I recommend using --limit flag to (well) limit the number of non-empty diffs displayed. Because without named arg (formula) the command will print all the diffs.

I recommend piping the output to bat or something like that, because the output is plain, no colorization.

+62 -0

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dawidd6

pr closed time in 4 days

pull request commentHomebrew/homebrew-linux-dev

cmd: add not-migrated command

Forgot about this PR. Will merge now.

dawidd6

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Pull request review commentHomebrew/homebrew-linux-dev

cmd: add not-migrated command

+# frozen_string_literal: true++require "cli/parser"+require "formula"++module Homebrew+  module_function++  def not_migrated_args+    Homebrew::CLI::Parser.new do+      usage_banner <<~EOS+        `not-migrated` [<formula>]++        Display not migrated Linux changes excluding bottles.+      EOS++      flag "--limit=",+           description: "Limit the number of non-empty diffs printed."+      flag "--homebrew-ref=",+           description: "Homebrew git ref (default `homebrew/master`)."+      flag "--linuxbrew-ref=",+           description: "Linuxbrew git ref (default `master`)."++      named_args max: 1+    end+  end++  def not_migrated+    args = not_migrated_args.parse++    homebrew_ref = args.homebrew_ref || "homebrew/master"+    linuxbrew_ref = args.linuxbrew_ref || "master"++    odie "Needs git >=2.30 to work" if Utils::Git.version < Version.parse("2.30")++    CoreTap.instance.path.cd do+      counter = 0+      formulae = if args.no_named?+        Formula+      else+        args.named.to_formulae+      end++      formulae.each do |formula|+        diff = Utils.safe_popen_read Utils::Git.path,+                                     "--no-pager", "diff",+                                     "-G", "unless OS.mac",+                                     "-I", "^ .*sha256 .+",

Added

dawidd6

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Pull request review commentHomebrew/homebrew-linux-dev

cmd: add not-migrated command

+# frozen_string_literal: true++require "cli/parser"+require "formula"++module Homebrew+  module_function++  def not_migrated_args+    Homebrew::CLI::Parser.new do+      usage_banner <<~EOS+        `not-migrated` [<formula>]++        Display not migrated Linux changes excluding bottles.+      EOS++      flag "--limit=",+           description: "Limit the number of non-empty diffs printed."+      flag "--homebrew-ref=",+           description: "Homebrew git ref (default `homebrew/master`)."+      flag "--linuxbrew-ref=",+           description: "Linuxbrew git ref (default `master`)."++      named_args max: 1+    end+  end++  def not_migrated+    args = not_migrated_args.parse++    homebrew_ref = args.homebrew_ref || "homebrew/master"+    linuxbrew_ref = args.linuxbrew_ref || "master"++    odie "Needs git >=2.30 to work" if Utils::Git.version < Version.parse("2.30")++    CoreTap.instance.path.cd do+      counter = 0+      formulae = if args.no_named?+        Formula+      else+        args.named.to_formulae+      end++      formulae.each do |formula|+        diff = Utils.safe_popen_read Utils::Git.path,+                                     "--no-pager", "diff",+                                     "-G", "unless OS.mac",

Removed

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Louis Bergelson

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gatk 4.2.0.0 (#1292) Use python@3.9.

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gatk: update 4.2.0.0 bottle.

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pull request commentbrewsci/homebrew-bio

gatk 4.2.0.0

I updated python to 3.9.

Here are the results of those commands. Nothing too wierd...

🐋 brew formula gatk
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio/Formula/gatk.rb
🐋 brew info gatk
brewsci/bio/gatk: stable 4.1.8.1 (bottled)
Genome Analysis Toolkit: Variant Discovery in High-Throughput Sequencing
https://software.broadinstitute.org/gatk
/usr/local/Cellar/gatk/4.2.0.0 (10 files, 462MB) *
  Built from source on 2021-02-22 at 14:44:03
From: https://github.com/brewsci/homebrew-bio/blob/HEAD/Formula/gatk.rb
License: BSD-3-Clause
==> Dependencies
Required: openjdk ✔, python@3.8 ✔
==> Caveats
This brew installation does not include the necessary python dependencies to run certain gatk tools.
Similarly, it does not install the necessary version of R and its packages for certain plotting functions to work.

See the GATK readme for detailed installation instructions.
   https://github.com/broadinstitute/gatk

The recommended way of running the tools with complex python dependencies is to use the pre-built docker images instead of attempting to install them locally.
Gatk dockers are available on docker hub:
   https://hub.docker.com/r/broadinstitute/gatk/tags/
lbergelson

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PR opened brewsci/homebrew-bio

krona 2.8 (new formula)
  • [x] Have you followed the guidelines for contributing?
  • [x] Have you checked that there aren't other open pull requests for the same formula update/change?
  • [x] Have you built your formula locally with brew install --build-from-source FORMULA, where FORMULA is the name of the formula you're submitting?
  • [x] Does your build pass brew audit --strict FORMULA (after doing brew install FORMULA)?

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pull request commentGFA-spec/GFA-spec

[DON'T MERGE] define walk line in GFA1

I was working on adding W-lines to gfabase, hit the following roadbump with SeqStart/SeqEnd: suppose user is asking to slice/subset the GFA to a specific region or series of bubbles. In some common cases, it'd be reasonable+useful to provide substrings of the Walks (namely, when a Walk has exactly one substring whose segments are all included in the subgraph). It's then however not straightforward to set SeqStart and SeqEnd in the sub-GFA:

  1. If we copy them as-is then they'd be misleading.
  2. We could attempt to recalculate them based on the lengths of the flanking excluded segments, but this seems dicey if the original sequence may have indels wrt the graph segments (not represented in the graph)
  3. They can't (as of this diff) be left missing.

If we could set them to missing, then I can always pile extra info in tags.

lh3

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viennarna 2.4.17: Upload the bottle (#1300)

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viennarna 2.4.17 (#1300)

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viennarna 2.4.17

Created with brew bump-formula-pr.

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Revert "Dockerfile: add gawk (#196)"

This reverts commit 62ad6b24ee9236c450a816734d47c17cd4a4b33f.

I actually need to add gawk to https://github.com/Homebrew/brew

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Revert "Dockerfile: add gawk (#196)"

This reverts commit 62ad6b24ee9236c450a816734d47c17cd4a4b33f.

I actually need to add gawk to https://github.com/Homebrew/brew

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Dockerfile: add gawk (#196) This is needed to build glibc

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Dockerfile: add gawk

This is needed to build glibc

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This is needed to build glibc

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