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Index: head/biology/Makefile
===================================================================
--- head/biology/Makefile
+++ head/biology/Makefile
@@ -41,6 +41,7 @@
SUBDIR += iqtree
SUBDIR += jalview
SUBDIR += jellyfish
+ SUBDIR += kallisto
SUBDIR += lagan
SUBDIR += lamarc
SUBDIR += libgtextutils
Index: head/biology/kallisto/Makefile
===================================================================
--- head/biology/kallisto/Makefile
+++ head/biology/kallisto/Makefile
@@ -0,0 +1,33 @@
+# $FreeBSD$
+
+PORTNAME= kallisto
+DISTVERSIONPREFIX= v
+DISTVERSION= 0.43.1
+CATEGORIES= biology
+
+MAINTAINER= jwb@FreeBSD.org
+COMMENT= Quantify abundances of transcripts from RNA-Seq data
+
+LICENSE= BSD2CLAUSE
+LICENSE_FILE= ${WRKSRC}/license.txt
+
+LIB_DEPENDS= libhdf5.so:science/hdf5 \
+ libsz.so:science/szip
+
+USES= cmake
+USE_GITHUB= yes
+GH_ACCOUNT= pachterlab
+
+SUB_FILES= kallisto-test
+
+PORTEXAMPLES= *
+PLIST_FILES= bin/kallisto
+EXAMPLES_PLIST_FILES= bin/kallisto-test
+
+OPTIONS_DEFINE= EXAMPLES
+
+post-install-EXAMPLES-on:
+ ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
+ cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
+
+.include <bsd.port.mk>
Index: head/biology/kallisto/distinfo
===================================================================
--- head/biology/kallisto/distinfo
+++ head/biology/kallisto/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1512166931
+SHA256 (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e
+SIZE (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 1067076
Index: head/biology/kallisto/files/kallisto-test.in
===================================================================
--- head/biology/kallisto/files/kallisto-test.in
+++ head/biology/kallisto/files/kallisto-test.in
@@ -0,0 +1,48 @@
+#!/bin/sh
+
+##########################################################################
+# Script description:
+#
+# Arguments:
+#
+# Returns:
+#
+# History:
+# Date Name Modification
+# 2016-03-21 Charlie & Begin
+##########################################################################
+
+usage()
+{
+ printf "Usage: $0 test-directory\n"
+ exit 1
+}
+
+
+##########################################################################
+# Main
+##########################################################################
+
+if [ $# != 1 ]; then
+ usage
+fi
+
+dir="$1"
+if [ -e "$dir" ]; then
+ printf "$dir already exists. Remove it first or choose a different name.\n"
+ exit 1
+fi
+
+cp -iR %%EXAMPLESDIR%% "$dir"
+cd "$dir"
+kallisto index -i transcripts.idx transcripts.fasta.gz
+kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
+ls -l output
+more output/abundance.tsv
+
+cat << EOM
+
+See https://pachterlab.github.io/kallisto/starting.html for instructions
+on interpreting the output above.
+
+EOM
Index: head/biology/kallisto/pkg-descr
===================================================================
--- head/biology/kallisto/pkg-descr
+++ head/biology/kallisto/pkg-descr
@@ -0,0 +1,6 @@
+Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
+data, or more generally of target sequences using high-throughput sequencing
+reads. It is based on the novel idea of pseudoalignment for rapidly determining
+the compatibility of reads with targets, without the need for alignment.
+
+WWW: https://pachterlab.github.io/kallisto/about.html

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