Add recipe for chexalign (#22663)

Co-authored-by: BiocondaBot <biocondabot@gmail.com>

recipes/chexalign/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+set -eu -o pipefail
+
+outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $outdir
+mkdir -p $PREFIX/bin
+
+cp ./chexalign_v0.11.jar $outdir
+cp $RECIPE_DIR/chexalign.sh $outdir/chexalign
+chmod +x $outdir/chexalign
+ln -s $outdir/chexalign $PREFIX/bin

recipes/chexalign/chexalign.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+# Wraps CHEXALIGN tool
+set -o pipefail
+
+# Find original directory of bash script, resolving symlinks.
+# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+SHARE_DIR=$DIR/..
+
+java=java
+JAR_DIR=$DIR
+
+if [ -z "${JAVA_HOME:=}" ]; then
+  if [ -e "$JAVA_HOME/bin/java" ]; then
+      java="$JAVA_HOME/bin/java"
+  fi
+fi
+
+# extract memory and system property Java arguments from the list of provided arguments
+# http://java.dzone.com/articles/better-java-shell-script
+default_jvm_mem_opts="-Xms512m -Xmx1g"
+jvm_mem_opts=""
+jvm_prop_opts=""
+pass_args=""
+for arg in "$@"; do
+    case $arg in
+        '-D'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+        '-XX'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+         '-Xm'*)
+            jvm_mem_opts="$jvm_mem_opts $arg"
+            ;;
+         *)
+            pass_args="$pass_args $arg"
+            ;;
+    esac
+done
+
+if [ "$jvm_mem_opts" == "" ]; then
+    jvm_mem_opts="$default_jvm_mem_opts"
+fi
+
+eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/chexalign_v0.11.jar" $pass_args
+
+exit

recipes/chexalign/meta.yaml

@@ -0,0 +1,28 @@
+{% set version="0.11" %}
+{% set sha256 = "7bcf3619f16bcd074bdacf80af6e760f22eb9301d08dee35ca21f6c5ec91b9f3" %}
+
+package:
+  name: chexalign
+  version: '{{ version }}'
+
+build:
+  noarch: generic
+  number: 0
+
+source:
+  url: http://lugh.bmb.psu.edu/software/chexalign/chexalign_v{{ version }}.jar
+  sha256: '{{ sha256 }}'
+
+requirements:
+  run:
+    - openjdk >=8
+
+test:
+  commands:
+    - chexalign --version 2>&1 | grep {{ version }}
+
+about:
+  home: https://github.com/seqcode/chexalign
+  license: MIT
+  summary: ChExAlign is used for alignment and quantification of ChIP-exo crosslinking patterns.
+  description: ChExAlign is a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. The output of the alignment approach is a set of composite profiles that represent the crosslinking signatures of the complex across analyzed regulatory regions. We then use a probabilistic mixture model to deconvolve individual crosslinking events within the aligned ChIP-exo profiles, enabling consistent measurements of protein-DNA crosslinking strengths across multiple proteins.