[ci skip] Merge PR 34374

Merge PR #34374, commits were: * Gah, what did I break? * Update build.sh * Update azure-pipeline.yml * Update azure-pipeline.yml * See if the CI is properly setting HOME now * Update azure-pipeline-master.yml * Update azure-pipeline.yml * add HOME to test as well * Update run_test.sh * Update build.sh * Update build.sh * try pre-fetching rust deps * Update build.sh * Update build.sh * Update run_test.sh * Merge branch 'bioconda:master' into master * Update verkko to v1.0 release
bioconda · Apr 21, 2022 · 1d0f441 · 1d0f441
1 parent 174bc74
commit 1d0f441
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Showing 6 changed files with 34 additions and 12 deletions.
diff --git a/azure-pipeline-master.yml b/azure-pipeline-master.yml
@@ -123,6 +123,7 @@ jobs:
 
       export OSTYPE="darwin"
       export CI="true"
+      export HOME=`pwd`
       bioconda-utils build recipes config.yml \
           --anaconda-upload \
           --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \

diff --git a/azure-pipeline.yml b/azure-pipeline.yml
@@ -180,6 +180,7 @@ stages:
 
         export OSTYPE="darwin"
         export CI="true"
+        export HOME=`pwd`
         bioconda-utils build recipes config.yml \
             --git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" HEAD
       displayName: Test

diff --git a/recipes/verkko/build.sh b/recipes/verkko/build.sh
@@ -1,5 +1,15 @@
 #!/bin/bash
-set -e
+set -ex
+
+# taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh
+if [ "$(uname)" == "Darwin" ]; then
+
+    # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory
+    export HOME=`pwd`
+    echo "HOME is $HOME"
+    mkdir -p $HOME/.cargo/registry/index/
+fi
+
 
 pushd src
 make clean && make -j$CPU_COUNT

diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml
@@ -6,28 +6,29 @@ package:
   version: {{ version }}
 
 source:
-  url: https://github.com/marbl/{{ name }}/releases/download/v{{ version }}_beta2/{{ name }}-v{{ version }}.tar.gz
-  md5: f8b71dfbcfcdfa31fce5c14f75f41ef7
+  url: https://github.com/marbl/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
+  md5: 3cb085c0e015f01f61be67ee80da632c
+
   patches:
     - version.patch
 
 build:
-  number: 2
-  skip: True # [osx]
+  number: 3
 
 requirements:
   build:
     - make
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - {{ compiler('cxx') }}
+    - rust
   host:
     - gsl
   run:
     - python >=3.7
-    - snakemake-minimal >=6.0.0
-    - graphaligner >=1.0.15
-    - mbg >=1.0.9
+    - snakemake-minimal >=7.0.0
+    - graphaligner >=1.0.16
+    - mbg >=1.0.10
 
 test:
   requires:

diff --git a/recipes/verkko/run_test.sh b/recipes/verkko/run_test.sh
@@ -1,13 +1,22 @@
 #!/bin/bash
 # stop on error
-set -eu -o pipefail
+set -exu -o pipefail
+
+# taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh
+if [ "$(uname)" == "Darwin" ]; then
+
+    # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory
+    export HOME=`pwd`
+    echo "HOME is $HOME"
+    mkdir -p $HOME/.cargo/registry/index/
+fi
 
 # download and run a small assembly
 
 rm -f ./hifi.fastq.gz ./ont.fastq.gz
 curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz
 curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz -o ont.fastq.gz
-verkko -d asm --correct-hash-bits 22 --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz
+verkko -d asm --no-correction --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz
 
 if [ ! -s asm/assembly.fasta ]; then
    echo "Error: verkko assembly test failed!"

diff --git a/recipes/verkko/version.patch b/recipes/verkko/version.patch
@@ -6,8 +6,8 @@ index 5f33ff4..25c2285 100644
  # Perform post-processing on global variables as needed.
  DEFS := $(addprefix -D,${DEFS})
  INCDIRS := $(addprefix -I,$(call CANONICAL_PATH,${INCDIRS}))
--VERSION := verkko release v1.0 beta2
-+VERSION := bioconda $(PKG_NAME) bioconda $(PKG_VERSION) beta2
+-VERSION := verkko release v1.0
++VERSION := bioconda $(PKG_NAME) bioconda $(PKG_VERSION)
 
  # Define the "all" target (which simply builds all user-defined targets) as the
  # default goal.