Added Dockerfile

Dockerfile

@@ -0,0 +1,24 @@
+FROM continuumio/miniconda:latest
+
+COPY environment.yml .
+RUN apt-get update -y && apt-get install -y zlib1g zlib1g-dev gcc 
+RUN conda update -n base -c defaults conda && \
+    conda env update --name base --file /environment.yml && \
+	rm /environment.yml
+
+COPY SNP/ /SNP
+WORKDIR /checkmate
+COPY patterngenerator/ .
+COPY ngscheckmate_fastq-source ./ngscheckmate_fastq-source
+COPY patterngenerator ./patterngenerator
+RUN cd ngscheckmate_fastq-source && alias cc=$(which gcc) && make
+RUN cd patterngenerator && make
+RUN chmod +x ngscheckmate_fastq-source/ngscheckmate_fastq && cp ngscheckmate_fastq-source/ngscheckmate_fastq /bin/ && cp ngscheckmate_fastq-source/ngscheckmate_fastq ./
+RUN chmod +x patterngenerator/patternconverter && cp patterngenerator/patternconverter /bin/ && cp patterngenerator/patternconverter ./
+
+COPY tests/ .
+COPY ncm_fastq.py ncm_test.py ncm.py /bin/
+
+RUN chmod +x /bin/ncm_fastq.py && chmod +x /bin/ncm.py
+
+ENV NCM_HOME /checkmate

README.md

@@ -84,9 +84,9 @@ export NCM_HOME=<installation_dir>/NGSCheckMate
 #### 2) Configuration (required only for the BAM module)
 If your input is BAM/VCF files, add the following lines in your ncm.conf file in the package directory. If your input is FASTQ files, you can skip this step.
 ```
-REF=<path for the reference FASTA file >  
-SAMTOOLS=<path for samtools> 
-BCFTOOLS=<path for bcftools>
+export REF=<path/to/reference>
+export SAMTOOLS=<path/to/samtools>
+export BCFTOOLS=<path/to/bcftools>
 ```
 
 #### Buid for fastq module / patterngenerator

environment.yml

@@ -0,0 +1,16 @@
+name: NGSCheckMate
+channels:
+    - anaconda
+    - conda-forge
+    - bioconda
+dependencies:
+    - python=2.7
+    - samtools=1.3.1
+    - bcftools=1.9
+    - make
+    - zlib
+    - gxx_linux-64
+    - pip
+    - pip:
+        - requests
+        - git+https://github.com/SimBioSysInc/MAFpy.git

ncm.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 import os
 import math
 import subprocess, time
@@ -1177,15 +1179,9 @@ def run_mpileup():
     else:
         print "WARNNING : NCM_HOME is not defined yet. Therefore, program will try to search ncm.conf file from the current directory"
         INSTALL_DIR=""
-    with open(INSTALL_DIR + "ncm.conf",'r') as F:
-        for line in F.readlines():
-            temp = line.split('=')
-	    if temp[0].startswith("SAMTOOLS"):
-                SAMTOOLS = temp[1].strip()
-            elif temp[0].startswith("BCFTOOLS"):
-                BCFTOOLS = temp[1].strip()
-            elif temp[0].startswith("REF"):
-                REF = temp[1].strip()
+    SAMTOOLS = os.environ.get("SAMTOOLS", False) or "samtools"
+    BCFTOOLS = os.environ.get("BCFTOOLS", False) or "bcftools"
+    REF= os.environ.get("BCFTOOLS", False)
 #    REF="/NAS/nas33-2/mpileup/hg19.fasta"
 
     version =""

ncm_fastq.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import os
 import sys
 import math

ncm_test.py

@@ -888,18 +888,10 @@ def remove_internal_files():
 def run_mpileup():
 
 
-    SAMTOOLS=""
-    BCFTOOLS=""
-    REF=""
-    with open("./ncm.conf",'r') as F:
-        for line in F.readlines():
-            temp = line.split('\"')
-	    if temp[0].startswith("SAMTOOLS"):
-                SAMTOOLS = temp[1].strip()
-            elif temp[0].startswith("BCFTOOLS"):
-                BCFTOOLS = temp[1].strip()
-            elif temp[0].startswith("REF"):
-                REF = temp[1].strip()
+    SAMTOOLS = os.environ.get("SAMTOOLS", False) or "samtools"
+    BCFTOOLS = os.environ.get("BCFTOOLS", False) or "bcftools"
+    REF= os.environ.get("BCFTOOLS", False)
+
 #    REF="/NAS/nas33-2/mpileup/hg19.fasta"
 
     for sample in bam_list:

ngscheckmate_fastq-source/Makefile

@@ -1,4 +1,4 @@
-COMPILER = gcc
+CC ?= gcc
 DFLAGS = 
 CFLAGS = -c
 OFLAGS = -lpthread -lm -lz -o
@@ -7,15 +7,15 @@ OFLAGS = -lpthread -lm -lz -o
 EXECNAME = ngscheckmate_fastq
 
 ngscheckmate:   stringhash2.o ngscheckmate_functions.o ngscheckmate_main.o
-	${COMPILER} ${DFLAGS} stringhash2.o ngscheckmate_functions.o ngscheckmate_main.o ${OFLAGS} ${EXECNAME}
+	${CC} ${DFLAGS} stringhash2.o ngscheckmate_functions.o ngscheckmate_main.o ${OFLAGS} ${EXECNAME}
 
 stringhash2.o:   stringhash2.c stringhash2.h
-	${COMPILER} ${DFLAGS} ${CFLAGS} stringhash2.c
+	${CC} ${DFLAGS} ${CFLAGS} stringhash2.c
 
 ngscheckmate_functions.o:   ngscheckmate_functions.c ngscheckmate.h patternconvert.h
-	${COMPILER} ${DFLAGS} ${CFLAGS} ngscheckmate_functions.c patternconvert.h
+	${CC} ${DFLAGS} ${CFLAGS} ngscheckmate_functions.c patternconvert.h
 
 ngscheckmate_main.o:     ngscheckmate_main.c ngscheckmate.h
-	${COMPILER} ${DFLAGS} ${CFLAGS} ngscheckmate_main.c
+	${CC} ${DFLAGS} ${CFLAGS} ngscheckmate_main.c
 
 

vaf_ncm.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import os
 import sys
 import math