Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 (#12549)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590

* Update install patch for 0.2.4

* Match nim release version 0.19.0

recipes/mosdepth/build.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-export BRANCH=v0.17.2
+export BRANCH=v0.19.0
 export PATH="nim-$BRANCH/bin/nim/bin:${PATH:+:$PATH}"
 bash ./scripts/install.sh
 export PATH="nim-$BRANCH/bin:${PATH:+:$PATH}"

recipes/mosdepth/install.diff

@@ -1,33 +1,29 @@
-diff --git a/scripts/install.sh b/scripts/install.sh
 --- a/scripts/install.sh
 +++ b/scripts/install.sh
-@@ -1,8 +1,5 @@
- #!/bin/bash
+@@ -6,25 +6,11 @@
+ set -euo pipefail
+ export base=$(pwd)
 
+-BRANCH=devel
+-
+-sudo apt-get update
 -sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
 -     curl  libssl-dev libtool autoconf automake libcurl4-openssl-dev
 -
- export base=$(pwd)
- if [ ! -x nim-$BRANCH/bin/nim ]; then
-   git clone -b $BRANCH --depth 1 git://github.com/nim-lang/nim nim-$BRANCH/
-@@ -23,7 +20,7 @@
-   fi
- fi
+ git clone -b $BRANCH --depth 1 git://github.com/nim-lang/nim nim-$BRANCH/
+ cd nim-$BRANCH
+ sh build_all.sh
 
--export PATH=$PATH:$base/nim-$BRANCH/bin/:$PATH:$base/nimble/src
-+export PATH=$base/nim-$BRANCH/bin/:$PATH:$base/nimble/src:$PATH
+-export PATH=$PATH:$base/nim-$BRANCH/bin/
++export PATH=$base/nim-$BRANCH/bin/:$PATH
  cd $base
- echo $PATH
-
-@@ -45,11 +42,3 @@
- set -x
- cd $base
- nimble install -y
+ nimble refresh
+ $base/nim-$BRANCH/bin/nimble install -y
+-
 -git clone --recursive https://github.com/samtools/htslib.git
 -
--cd htslib && git checkout 1.5 && autoheader && autoconf && ./configure --enable-libcurl
+-cd htslib && git checkout 1.9 && autoheader && autoconf && ./configure --enable-libcurl
 -cd ..
 -make -j 4 -C htslib
 -export LD_LIBRARY_PATH=$base/htslib
 -ls -lh $base/htslib/*.so
--echo $base

recipes/mosdepth/meta.yaml

@@ -1,7 +1,7 @@
 {% set name = "mosdepth" %}
-{% set version = "0.2.3" %}
+{% set version = "0.2.4" %}
 #{% set revision = "9a9ef85" %}
-{% set sha256hash = "a05b3ef3c779c2155816954322adca2d7c06b3e19a409993020b9ad4bbd28dd4" %}
+{% set sha256hash = "e49f1e2973f0016aa1f93fffa2b050a2f320faf552f790f6edd60c9e86edfe18" %}
 
 package:
   name: {{ name|lower }}
@@ -14,7 +14,7 @@ source:
     - install.diff
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx]
 
 requirements: