Update ncbi-vdb to 3.0.0 (bioconda#33449)

* Update ncbi-vdb to 2.11.1 * Update meta.yaml * Update build.sh * Update ncbi-vdb to 2.11.2 * Update ncbi-vdb to 3.0.0 * decrease OSX workers * Update ncbi-vdb to 3.0.0 * debug * OK * recursive * update header copying Co-authored-by: Robert A. Petit III <[email protected]> Co-authored-by: Maarten-vd-Sande <[email protected]> Co-authored-by: Devon Ryan <[email protected]>
jscaber · Mar 2, 2022 · 8bcbce0 · 8bcbce0
1 parent 29a450a
commit 8bcbce0
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Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml
@@ -60,7 +60,7 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        runner: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+        runner: [0, 1, 2, 3, 4, 5, 6, 7]
     steps:
     - uses: actions/checkout@v1
 
@@ -117,6 +117,6 @@ jobs:
         python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
         echo '============'
         bioconda-utils build recipes config.yml \
-          --worker-offset ${{ matrix.runner }} --n-workers 10 \
+          --worker-offset ${{ matrix.runner }} --n-workers 8 \
           --anaconda-upload
         conda clean -y --all
diff --git a/recipes/ncbi-vdb/build.sh b/recipes/ncbi-vdb/build.sh
@@ -1,3 +1,5 @@
+#!/bin/bash
+set -e
 # For inspiration, see also Debian's ncbi-vdb package:
 # https://salsa.debian.org/med-team/ncbi-vdb
 
@@ -12,11 +14,11 @@ sed -i.backup \
 
 # * --debug lets the configure script print extra info
 # * Only LDFLAGS and CXX can be customized at configure time.
+./configure --help
 ./configure \
     --debug \
     --prefix=$PREFIX \
     --build-prefix=ncbi-outdir \
-    --with-ngs-sdk-prefix=$PREFIX \
     CXX=$CXX
 
 # Edit the generated build configuration to use the proper tools
@@ -27,7 +29,7 @@ sed -i.backup \
 #     -e "s|= ar|= $AR|" \
 #     build/Makefile.config.linux.x86_64
 
-make
+make CC=$CC
 
 # This does not install the header files
 make install
@@ -36,7 +38,10 @@ make install
 make -C test/vdb
 
 # Copy headers manually. As done by Debian, install them into a common subdirectory
-mv interfaces/* $PREFIX/include/ncbi-vdb
+ls interfaces
+for f in interfaces/* ; do
+    mv $f $PREFIX/include/ncbi-vdb
+done
 
 
 # To Do

diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.11.0" %}
-{% set sha256 = "9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa" %}
+{% set version = "3.0.0" %}
+{% set sha256 = "154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7" %}
 
 package:
   name: ncbi-vdb
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
 
 source:
   url: https://github.com/ncbi/ncbi-vdb/archive/{{ version }}.tar.gz
@@ -20,6 +20,7 @@ source:
 requirements:
   build:
     - make
+    - cmake
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
   host: