Add recipe for fusioncatcher

recipes/fusioncatcher/build.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# copy main scripts
+chmod +x bin/*.py
+cp bin/* ${PREFIX}/bin/
+cp etc/configuration.cfg ${PREFIX}/etc/
+
+# copy script to download database
+chmod +x ${RECIPE_DIR}/download-db.sh
+cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin
+
+# create folder for database download
+target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}
+mkdir -p ${target}/db/
+touch ${target}/db/.empty
+
+# set FC DB PATH variable on env activation
+mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d
+cat <<EOF >> ${PREFIX}/etc/conda/activate.d/fusioncatcher.sh
+export FC_DB_PATH=${target}/db/
+EOF
+
+cat <<EOF >> ${PREFIX}/etc/conda/deactivate.d/fusioncatcher.sh
+unset FC_DB_PATH
+EOF

recipes/fusioncatcher/download-db.sh

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+echo "Downloading Human Ensembl v90 database to ${FC_DB_PATH}/current/..."
+
+# Direct download:
+cd ${FC_DB_PATH}
+rm -rf human_v90.tar.gz.*
+wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.aa
+wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.ab
+wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.ac
+wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.ad
+cat human_v90.tar.gz.* | tar xz
+ln -s human_v90 current
+
+echo "Human Ensembl v90 database is downloaded."
+
+exit 0

recipes/fusioncatcher/meta.yaml

@@ -0,0 +1,89 @@
+{% set name = "fusioncatcher" %}
+{% set version = "1.00" %}
+{% set sha256 = "46cd7ab4f06160b9735b03893254171ecc387d35c12796998448cd1594775dbc" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://sourceforge.net/projects/{{ name }}/files/{{ name }}_v{{ version }}.zip
+  sha256: {{ sha256 }}
+  patches:
+    - paths.patch
+
+build:
+  number: 0
+  skip: True  # [py3k]
+
+requirements:
+  host:
+    - python
+    - biopython >=1.50
+    - bowtie=1.2.0
+    - fusioncatcher-seqtk=1.2
+    - star=2.5.2b
+    - bowtie2=2.3.0
+    - bbmap
+    - blat=35
+    - lzo
+    - bwa=0.7.12
+    - ucsc-faToTwoBit 
+    - velvet=1.2.10
+    - openpyxl=2.5.0a2
+    - xlrd=1.0.0
+    - pigz=2.3
+    - samtools=0.1.19
+    - picard=2.10.6
+    - numpy=1.13.1
+    - parallel=20171222
+    - ucsc-liftover
+    - oases
+    - lzop
+    - java-jdk
+    - sra-tools=2.6.2
+    - zip
+  run:
+    - python
+    - biopython >=1.50
+    - bowtie=1.2.0
+    - fusioncatcher-seqtk=1.2
+    - star=2.5.2b
+    - bowtie2=2.3.0
+    - bbmap
+    - blat=35
+    - lzo
+    - bwa=0.7.12
+    - ucsc-faToTwoBit 
+    - velvet=1.2.10
+    - openpyxl=2.5.0a2
+    - xlrd=1.0.0
+    - pigz=2.3
+    - samtools=0.1.19
+    - picard=2.10.6
+    - numpy=1.13.1
+    - parallel=20171222
+    - ucsc-liftover
+    - oases
+    - lzop
+    - java-jdk
+    - sra-tools=2.6.2
+    - zip
+
+test:
+  commands:
+    - export FC_DB_PATH=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/db && fusioncatcher -h
+    - export FC_DB_PATH=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/db && fusioncatcher-build -h
+
+about:
+  home: https://github.com/ndaniel/fusioncatcher
+  license: GPL-3.0
+  summary: "Finder of Somatic Fusion Genes in RNA-seq data."
+  license_family: GPL
+  license_file: LICENSE
+
+extra:
+  identifiers:
+    - doi:10.1101/011650
+  skip-lints:
+    - uses_javajdk

recipes/fusioncatcher/paths.patch

@@ -0,0 +1,100 @@
+--- etc/configuration.cfg	2018-10-17 18:23:40.361288543 -0500
++++ etc/configuration.cfg.new	2018-10-17 18:46:16.142296785 -0500
+@@ -1,37 +1,35 @@
+ [paths]
+-python = /usr/bin/
++python = ${CONDA_PREFIX}/bin/
+ #
+ # for changing the shebang for all Python scripts used by FusionCatcher 
+ # to '#!/some/other/python'
+ # one could run 'fusioncatcher/bin/shebang.py' -s #!/some/other/python
+ #
+-data = /apps/fusioncatcher/data/current/
+-scripts = /apps/fusioncatcher/bin/
+-bowtie = /apps/fusioncatcher/tools/bowtie/
+-bowtie2 = /apps/fusioncatcher/tools/bowtie2/
+-blat = /apps/fusioncatcher/tools/blat/
+-bwa = /apps/fusioncatcher/tools/bwa/
+-bbmap = /apps/fusioncatcher/tools/bbmap/
+-liftover = /apps/fusioncatcher/tools/liftover/
+-velvet = /apps/fusioncatcher/tools/velvet/
+-oases = /apps/fusioncatcher/tools/oases/
+-fatotwobit = /apps/fusioncatcher/tools/blat/
+-samtools = /apps/fusioncatcher/tools/samtools/
+-seqtk = /apps/fusioncatcher/tools/seqtk/
+-star = /apps/fusioncatcher/tools/star/source/
+-sra = /apps/fusioncatcher/tools/sratoolkit/bin/
+-numpy = /apps/fusioncatcher/tools/numpy/
+-biopython = /apps/fusioncatcher/tools/biopython/
+-xlrd = /apps/fusioncatcher/tools/xlrd/
+-openpyxl = /apps/fusioncatcher/tools/openpyxl/
+-lzo = /apps/fusioncatcher/tools/lzo/
+-lzop = /apps/fusioncatcher/tools/lzop/src/
+-coreutils = /apps/fusioncatcher/tools/coreutils/src/
+-parallel = /appsfusioncatcher/tools/paralell/src/
+-pigz = /apps/fusioncatcher/tools/pigz/
+-pxz = /apps/fusioncatcher/tools/pxz/
+-picard = /apps/fusioncatcher/tools/picard/
+-java = /usr/bin/
++data = ${FC_DB_PATH}/current/
++scripts = ${CONDA_PREFIX}/bin/
++bowtie =  ${CONDA_PREFIX}/bin/
++bowtie2 =  ${CONDA_PREFIX}/bin/
++blat =  ${CONDA_PREFIX}/bin/
++bwa =  ${CONDA_PREFIX}/bin/
++bbmap =  ${CONDA_PREFIX}/bin/
++liftover = ${CONDA_PREFIX}/bin/  
++velvet =  ${CONDA_PREFIX}/bin/
++oases =  ${CONDA_PREFIX}/bin/
++fatotwobit =  ${CONDA_PREFIX}/bin/
++samtools =  ${CONDA_PREFIX}/bin/
++seqtk =  ${CONDA_PREFIX}/bin/
++star =  ${CONDA_PREFIX}/bin/
++sra = ${CONDA_PREFIX}/bin/
++numpy = ${CONDA_PREFIX}/lib/python*/site-packages/numpy/
++biopython = ${CONDA_PREFIX}/lib/python*/site-packages/
++xlrd = ${CONDA_PREFIX}/lib/python*/site-packages/xlrd/
++openpyxl = ${CONDA_PREFIX}/lib/python*/site-packages/openpyxl/
++lzop = ${CONDA_PREFIX}/bin/
++coreutils = ${CONDA_PREFIX}/bin/
++parallel = ${CONDA_PREFIX}/bin/
++pigz = ${CONDA_PREFIX}/bin/
++picard = ${CONDA_PREFIX}/bin/
++java = ${CONDA_PREFIX}/bin/
+
+ [parameters]
+ threads = 0
+@@ -39,9 +37,3 @@
+
+ [versions]
+ fusioncatcher = 1.00
+-
+-
+-
+-
+-
+-
+--- bin/sort_ttdb.py	2018-10-17 18:23:40.372288599 -0500
++++ bin/sort_ttdb.py.new	2018-10-17 18:23:40.378288630 -0500
+@@ -1,4 +1,4 @@
+-#!/mnt/software/bin/python2.7-real
++#!/usr/bin/env python
+ # -*- coding: utf-8 -*-
+ """
+ It sorts the input file (text tab separated file) based on the specified columns.
+--- bin/add_custom_gene.py	2018-10-17 18:23:40.362288548 -0500
++++ bin/add_custom_gene.py.new	2018-10-17 18:23:40.377288625 -0500
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # -*- coding: utf-8 -*-
+ """
+ Add the custom human genes which are missing from the Ensembl database.
+--- bin/add_gap_gene.py	2018-10-17 18:23:40.371288594 -0500
++++ bin/add_gap_gene.py.new	2018-10-17 18:23:40.377288625 -0500
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # -*- coding: utf-8 -*-
+ """
+ Add the custom human genes which are known to have random inserts at fusion junction.

recipes/fusioncatcher/post-link.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+cat <<EOF >> ${PREFIX}/.messages.txt
+
+Please run download-db.sh to download the Human Ensembl v90 database to ${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/db/current/.
+If you have a custom database, please use "fusioncatcher" with the option "--data".
+
+EOF