Added recipe for kinSimRiboswitch (#10838)

Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.

recipes/kinsimriboswitch/activate.sh

@@ -0,0 +1,27 @@
+#!/bin/sh
+
+# Unset the passed env var <myvar>, backing up its value in BAK_<myvar>.
+backup_env_var() {
+    local var_name
+    var_name="$1"
+
+    # Var defined and value given, or defined and NO value given
+    if [ -n "${!var_name}" ] || [ -z "${!var_name-foo}" ]; then
+        export BAK_$var_name="${!var_name}"
+        unset $var_name
+    fi
+}
+
+backup_env_var PERL5LIB
+# backup_env_var PERL_MM_OPT
+# backup_env_var PERL_MB_OPT
+
+export PERL5LIB="$PREFIX/lib/perl5_custom:$PERL5LIB"
+
+
+
+
+
+# Set env vars, cf.
+# https://conda.io/docs/user-guide/tasks/manage-environments.html#saving-environment-variables
+

recipes/kinsimriboswitch/build.sh

@@ -0,0 +1,79 @@
+#!/bin/bash
+
+##############################################################################
+##                           Function definitions                           ##
+##############################################################################
+
+# Install a Perl distribution from a local source tarball.
+# Copied from conda skeleton cpan's build.sh + tar calls.
+install_perl_dist_tarball () {
+    local dist_tarball="$1"
+    if [ ! -s "$dist_tarball" ]; then
+        echo "Distribution tarball '$dist_tarball' empty or non-existent."
+        exit 1
+    fi
+
+    tar -xzf "$dist_tarball"
+    cd "${dist_tarball%.tar.gz}"
+
+    if [ -f Build.PL ]; then
+        perl Build.PL
+        perl ./Build
+        perl ./Build test
+        perl ./Build install --installdirs site
+    elif [ -f Makefile.PL ]; then
+        perl Makefile.PL INSTALLDIRS=site
+        make
+        make test
+        make install
+    else
+        echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.'
+        exit 1
+    fi
+
+    cd ..
+}
+
+install_bins () {
+    cp "$@" "$PREFIX/bin/"
+}
+
+##############################################################################
+##                                   Main                                   ##
+##############################################################################
+
+mkdir -p "$PREFIX/bin"
+mkdir -p "$PREFIX/lib"
+
+# Install binaries
+install_bins "$SRC_DIR"/bin/*
+
+# Install patched barriers
+tar -xzf 'Barriers-1.5.2.tar.gz'
+cd 'Barriers-1.5.2'
+./configure
+make
+make check
+install_bins 'barriers-RNA2'
+cd ..
+
+# Install patched Heap::Priority from local file
+install_perl_dist_tarball 'Heap-Priority-0.11-mod.tar.gz'
+
+# Install distribution-less Perl module RNAhelper.pm
+mkdir -p "$PREFIX/lib/perl5_custom"
+# Make sure this path is added to PERL5LIB in activate script!
+cp "$SRC_DIR"/lib/perl5/* "$PREFIX/lib/perl5_custom/"
+
+# Deploy activation / deactivation scripts
+mkdir -p "$PREFIX/etc/conda/activate.d"
+cp "$RECIPE_DIR/activate.sh" "$PREFIX/etc/conda/activate.d/$PKG_NAME-setenv.sh"
+mkdir -p "$PREFIX/etc/conda/deactivate.d"
+cp "$RECIPE_DIR/deactivate.sh" "$PREFIX/etc/conda/deactivate.d/$PKG_NAME-restoreenv.sh"
+
+# Run tests
+source "$RECIPE_DIR/activate.sh"           # make sure custom Perl modules are found
+# make test # TODO enable
+source "$RECIPE_DIR/deactivate.sh"         # make sure custom Perl modules are found
+
+# EOF

recipes/kinsimriboswitch/deactivate.sh

@@ -0,0 +1,21 @@
+#!/bin/sh
+
+# Restore the value of passed env var <myvar> from a backup variable
+# BAK_<myvar> and unset the backup variable.
+restore_env_var() {
+    local var_name
+    local bak_var_name
+    var_name="${1}"
+    bak_var_name="BAK_$var_name"
+
+    # Var defined and value given, or defined and NO value given
+    if [ -n "${!bak_var_name}" ] || [ -z "${!bak_var_name-foo}" ]; then
+        export $var_name="${!bak_var_name}"
+        unset $bak_var_name
+    fi
+}
+
+restore_env_var PERL5LIB
+# restore_env_var PERL_MM_OPT
+# restore_env_var PERL_MB_OPT
+

recipes/kinsimriboswitch/meta.yaml

@@ -0,0 +1,84 @@
+{% set version = '0.3' %}
+{% set hash = '51ade0550b2163d4766ccaa12a361f05b910b38b373ccb2ff08df0aac2193c1b' %}
+
+package:
+  name: kinsimriboswitch
+  version: {{ version }}
+
+source:
+    url: http://www.bioinf.uni-leipzig.de/~felix/downloads/software/kinSimRiboswitch-{{version}}.tar.gz
+    sha256: {{ hash }}
+
+build:
+  number: 0
+  skip: true # [win]
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - make
+  host:
+    - check
+    - perl
+    - perl-sys-info
+    - perl-parallel-loops
+    - perl-file-slurp
+    - perl-math-random-mt-auto
+    - perl-math-round
+    - perl-devel-assert
+    - perl-inline
+    - perl-inline-c
+    - perl-ipc-system-simple
+    - perl-list-moreutils
+    - perl-clone
+    - perl-parse-recdescent
+    - perl-heap
+    - r
+    - r-argparser
+    - r-rcolorbrewer
+    - viennarna
+    - treekin
+    - coreutils # need an up-to-date GNU sort
+    - gmp       # fixes strange segfault of coreutils' expr (missing libgmp)
+    - tar
+    - perl-extutils-makemaker
+  run:
+    - perl
+    - perl-sys-info
+    - perl-parallel-loops
+    - perl-file-slurp
+    - perl-math-random-mt-auto
+    - perl-math-round
+    - perl-devel-assert
+    - perl-inline
+    - perl-inline-c
+    - perl-ipc-system-simple
+    - perl-list-moreutils
+    - perl-clone
+    - perl-parse-recdescent
+    - perl-heap
+    - r
+    - r-argparser
+    - r-rcolorbrewer
+    - viennarna
+    - treekin
+    - coreutils
+#   - gmp       # Fix strange crash of conda build
+
+test:
+  commands:
+    - kinSimRiboswitch -h 1>/dev/null
+# imports:
+#   - RNAhelper         # perl module, TODO
+
+
+about:
+  home: http://www.bioinf.uni-leipzig.de/~felix/
+  license: GPLv3
+  license_file: COPYING
+  summary: |
+    Pipeline for the simulation of RNA--ligand interaction kinetics as
+    outlined in Kuehnl et al. 2017, https://doi.org/10.1186/s12859-017-1823-5
+
+