Schmutzi recipe

recipes/schmutzi/build.sh

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+#!/bin/bash
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
+
+#Adust path to copy executables too with prefix
+sed -i.bak "s#usr/bin/#${PREFIX}/bin#g" Makefile
+sed -i.bak "s#usr/share/#${PREFIX}/share#g" Makefile
+
+# Fix shebangs
+sed -i.bak "s:usr/bin/perl:usr/bin/env perl:" src/*.pl
+
+#Create dir for shared reference files
+mkdir -p $PREFIX/share
+
+# schmutzi uses non-standard bamtools functions that aren't part of the normal library
+cd lib
+rmdir bamtools
+git clone https://github.com/pezmaster31/bamtools
+mkdir bamtools/build
+cd bamtools/build
+cmake ..
+make
+cd ../..
+
+# Build libgab
+rmdir libgab
+git clone https://github.com/grenaud/libgab
+cd libgab
+make BAMTOOLSINC=${PREFIX}/include/bamtools BAMTOOLSLIB=${PREFIX}/lib
+#Copy libgab header files to include directories (?)
+cp -fv *.h ${PREFIX}/include/
+cp -fv *.o ${PREFIX}/lib/
+
+cd ../..
+
+
+
+make install
+

recipes/schmutzi/meta.yaml

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+{% set version = "1.5.5.5" %}
+package:
+  name: schmutzi
+  version: {{ version }}
+
+build:
+  number: 0 
+
+source:
+  url: https://github.com/grenaud/schmutzi/archive/{{ version }}.tar.gz
+  md5: b2c15b64a24aa1c52cd52bd30e9b92b3 
+  patches:
+    - patch
+    - patch2
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - jsoncpp
+  host:
+    - cmake
+    - bamtools
+    - git
+    - zlib
+    - jsoncpp
+  run:
+    - zlib
+    - perl
+    - jsoncpp
+    - r-base 
+    - r-fitdistrplus
+
+test:
+  commands:
+    - contDeam
+    - endoCaller
+    - mtCont
+    - approxDist.R
+    - schmutzi.pl
+    - bam2prof
+    - insertSize
+    - log2freq
+    - logs2pos
+    - mitoConsPDF.R
+    - msa2freq
+    - msa2log
+    - posteriorDeam.R
+    - contOut2ContEst.pl
+    - log2fasta
+
+
+about:
+  home: https://github.com/grenaud/schmutzi
+  license: unknown
+  summary: Maximum a posteriori estimate of contamination for ancient samples.

recipes/schmutzi/patch

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+--- src/splitEndoVsCont/Makefile	2018-07-19 11:54:29.000000000 +0200
++++ src/splitEndoVsCont/Makefile	2018-07-22 20:06:46.621001003 +0200
+@@ -1,5 +1,4 @@
+
+-CXX      = /usr/bin/g++ # -g -pg
+ BAMTOOLS = ../../lib/bamtools/
+ LIBGAB   = ../../lib/libgab/
+

recipes/schmutzi/patch2

@@ -0,0 +1,7 @@
+--- src/Makefile	2018-07-19 11:54:29.000000000 +0200
++++ src/Makefile	2018-07-22 19:12:20.599743706 +0200
+@@ -1,4 +1,3 @@
+-CXX      = /usr/bin/g++ #-g -pg
+ BAMTOOLS = ../lib/bamtools/
+ LIBGAB   = ../lib/libgab/
+