1st amap

recipes/amap/build.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#
+# CONDA build script variables 
+# 
+# $PREFIX The install prefix
+# $PKG_NAME The name of the package
+# $PKG_VERSION The version of the package
+# $PKG_BUILDNUM The build number of the package
+#
+set -eu -o pipefail
+
+cd align
+make
+
+mkdir -p $PREFIX/bin
+cp amap $PREFIX/bin

recipes/amap/meta.yaml

@@ -0,0 +1,36 @@
+{% set version = "2.2" %}
+
+package:
+  name: amap
+  version: {{ version }}
+
+build:
+  number: 0
+
+source:
+  url: https://github.com/mes5k/amap-align/archive/600fc29fb9d0e8a6abf797c173c7a416ab99c541.zip
+  sha256: 57391561dfa0ec0e291a11f54177cfcf17baa47be065f0cc688e4bb98de792b4
+  patches:
+    - patch.file 
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+
+  run:
+    - blast
+
+test:
+  commands:
+    - amap -gui
+
+about:
+  home: https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/
+  license: GPL-2
+  license_file: license/License.txt
+  summary: AMAP is a multiple sequence alignment program based on sequence annealing.
+  dev_url: https://github.com/mes5k/amap-align
+
+extra:
+  identifiers:
+    - doi:10.1093/bioinformatics/btl311

recipes/amap/patch.file

@@ -0,0 +1,24 @@
+diff -ruN amap_raw/align/Amap.cc amap_new/align/Amap.cc
+--- amap_raw/align/Amap.cc	2008-02-13 15:36:30.000000000 +0100
++++ amap_new/align/Amap.cc	2019-04-17 23:32:47.000000000 +0200
+@@ -23,6 +23,8 @@
+ #include <cstdlib>
+ #include <cerrno>
+ #include <iomanip>
++#include <cstring>  //BUG strcmp
++#include <climits>
+
+ string parametersInputFilename = "";
+ string parametersOutputFilename = "no training";
+diff -ruN amap_raw/align/Makefile amap_new/align/Makefile
+--- amap_raw/align/Makefile	2008-02-13 15:36:30.000000000 +0100
++++ amap_new/align/Makefile	2019-04-17 23:32:49.000000000 +0200
+@@ -6,7 +6,7 @@
+ # 1) Choose C++ compiler.
+ ################################################################################
+
+-CXX = g++
++# CXX = g++
+
+ ################################################################################
+ # 2) Set C++ flags.