From 60acc69c7592a2caffee5b03ec4a7bbe63b7445f Mon Sep 17 00:00:00 2001
From: Joerg Fallmann <jfallmann@users.noreply.github.com>
Date: Fri, 2 Nov 2018 23:49:14 +0100
Subject: [PATCH] Updated segemehl 0.2 added segemehl 0.3 (#11753)

* Updated segemehl 0.2 added segemehl 0.3

* Update meta.yaml

* skipping osx for now
---
 recipes/segemehl/0.2.0/build.sh  | 13 +++++++++++
 recipes/segemehl/0.2.0/meta.yaml | 40 ++++++++++++++++++++++++++++++++
 recipes/segemehl/build.sh        |  6 ++---
 recipes/segemehl/meta.yaml       | 26 +++++++++++++++------
 4 files changed, 75 insertions(+), 10 deletions(-)
 create mode 100644 recipes/segemehl/0.2.0/build.sh
 create mode 100644 recipes/segemehl/0.2.0/meta.yaml

diff --git a/recipes/segemehl/0.2.0/build.sh b/recipes/segemehl/0.2.0/build.sh
new file mode 100644
index 0000000000000..6901dfb4b2577
--- /dev/null
+++ b/recipes/segemehl/0.2.0/build.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+export C_INCLUDE_PATH=${PREFIX}/include:${PREFIX}/include/ncurses
+export LIBRARY_PATH=${PREFIX}/lib
+
+cd segemehl
+make segemehl.x -j${CPU_COUNT}
+make testrealign.x -j${CPU_COUNT}
+make lack.x -j${CPU_COUNT}
+
+for i in *.x ; do
+    install ${i} ${PREFIX}/bin
+done
diff --git a/recipes/segemehl/0.2.0/meta.yaml b/recipes/segemehl/0.2.0/meta.yaml
new file mode 100644
index 0000000000000..335c906221a8a
--- /dev/null
+++ b/recipes/segemehl/0.2.0/meta.yaml
@@ -0,0 +1,40 @@
+package:
+  name: segemehl
+  version: 0.2.0
+
+about:
+  home: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+  summary: Short read mapping with gaps
+build:
+  number: 5
+  skip: True  # [osx]
+  
+source:
+  url: "http://www.bioinf.uni-leipzig.de/Software/segemehl/old/segemehl_0_2_0.tar.gz"
+  sha256: 2575139d2f2ba7bd534afcbe485c0570c177d1faaeb267c4cd873e65b8e72afb
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - ncurses
+  run:
+    - ncurses
+
+test:
+  commands:
+    - segemehl.x --help 2>&1 | grep -A1 VERSION
+    - lack.x --help 2>&1 | grep -A1 VERSION
+    - testrealign.x --help 2>&1 | grep -A1 VERSION
+
+extra:
+  identifiers:
+    - biotools:segemehl
+
+about:
+  home: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+  license: GPL3
+#  license_file: licence.txt
+  summary: Short read mapping with gaps
diff --git a/recipes/segemehl/build.sh b/recipes/segemehl/build.sh
index 6bec800869269..fcd8ffe389b33 100644
--- a/recipes/segemehl/build.sh
+++ b/recipes/segemehl/build.sh
@@ -1,10 +1,10 @@
-#!/bin/sh
-cd segemehl
+#!/bin/bash
 
 export C_INCLUDE_PATH=${PREFIX}/include:${PREFIX}/include/ncurses
 export LIBRARY_PATH=${PREFIX}/lib
+export PKG_CONFIG_PATH=${PREFIX}/lib/pkgconfig
 
-make -j 1 ## do not use >1 make threads!
+make all -j${CPU_COUNT}  ## do not use >1 make threads!
 
 for i in *.x ; do
     install ${i} ${PREFIX}/bin
diff --git a/recipes/segemehl/meta.yaml b/recipes/segemehl/meta.yaml
index 9373bb6d9955e..b3dc824fdede0 100644
--- a/recipes/segemehl/meta.yaml
+++ b/recipes/segemehl/meta.yaml
@@ -1,33 +1,45 @@
+{% set version = "0.3.1" %}
+{% set sha256 = "04b6d92a118b897c8c7d1157c60b2671975cd21da17fe2b7e0200b83f8534c2b" %}
+
 package:
   name: segemehl
-  version: 0.2.0
+  version: {{ version }}
 
 about:
   home: http://www.bioinf.uni-leipzig.de/Software/segemehl/
   summary: Short read mapping with gaps
 build:
-  number: 4
+  number: 0
+  skip: True  # [osx]
 
 source:
-  url: "http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_2_0.tar.gz"
-  sha256: 2575139d2f2ba7bd534afcbe485c0570c177d1faaeb267c4cd873e65b8e72afb
+  url: "http://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/segemehl.tar.gz"
+  sha256: {{ sha256 }}
 
 requirements:
   build:
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - pkg-config
   host:
     - zlib
     - ncurses
+    - htslib
   run:
-    - zlib
     - ncurses
+    - htslib
 
 test:
   commands:
     - segemehl.x --help 2>&1 | grep -A1 VERSION
-    - lack.x --help 2>&1 | grep -A1 VERSION
-    - testrealign.x --help 2>&1 | grep -A1 VERSION
+    - haarz.x --help 2>&1 | grep -A1 VERSION
 
 extra:
   identifiers:
     - biotools:segemehl
+
+about:
+  home: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+  license: GPL3
+  license_file: licence.txt
+  summary: Short read mapping with gaps