Solve merge conflict

src/.conda_envs/umitools_0.3.4

+/Xnfs/lbmcdb/common/conda/envs/umitools_0.3.4
\ No newline at end of file

src/.conda_envs/urqt_d62c1f8

+/Xnfs/lbmcdb/common/conda/envs/urqt_d62c1f8
\ No newline at end of file

src/.conda_packages.sh

+source src/.conda_psmn.sh
+CONDA_ENVS=src/.conda_envs/
+if [ ! -d ${CONDA_ENVS}pigz_2.3.4 ]; then
+  conda create --yes --name pigz_2.3.4 pigz=2.3.4
+fi
+if [ ! -d ${CONDA_ENVS}tophat_2.1.1 ]; then
+  conda create --yes --name tophat_2.1.1 tophat=2.1.1
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.0.0 ]; then
+  conda create --yes --name hisat2_2.0.0 hisat2=2.0.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.1.0 ]; then
+  conda create --yes --name hisat2_2.1.0 hisat2=2.1.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.1 ]; then
+  conda create --yes --name rsem_1.3.1 rsem=1.3.1 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.0 ]; then
+  conda create --yes --name rsem_1.3.0 rsem=1.3.0 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}samblaster_0.1.24 ]; then
+  conda create --yes --name samblaster_0.1.24 samblaster=0.1.24
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.25.1 ]; then
+  conda create --yes --name nextflow_0.25.1 nextflow=0.25.1
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_19.01.0 ]; then
+  conda create --yes --name nextflow_19.01.0 nextflow=19.01.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.32.0 ]; then
+  conda create --yes --name nextflow_0.32.0 nextflow=0.32.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.28.2 ]; then
+  conda create --yes --name nextflow_0.28.2 nextflow=0.28.2
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.7 ]; then
+  conda create --yes --name samtools_1.7 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.5 ]; then
+  conda create --yes --name samtools_1.5 samtools=1.5
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.2 ]; then
+  conda create --yes --name bowtie2_2.3.2 bowtie2=2.3.2 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
+  conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
+fi
+if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
+  conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.36 ]; then
+  conda create --yes --name trimmomatic_0.36 trimmomatic=0.36
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.39 ]; then
+  conda create --yes --name trimmomatic_0.39 trimmomatic=0.39
+fi
+if [ ! -d ${CONDA_ENVS}Python_3.6.1 ]; then
+  conda create --yes --name Python_3.6.1 Python=3.6.1
+fi
+if [ ! -d ${CONDA_ENVS}Python_2.7.13 ]; then
+  conda create --yes --name Python_2.7.13 Python=2.7.13
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.44.0 ]; then
+  conda create --yes --name kallisto_0.44.0 kallisto=0.44.0
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.43.1 ]; then
+  conda create --yes --name kallisto_0.43.1 kallisto=0.43.1
+fi
+if [ ! -d ${CONDA_ENVS}music_1.0.0 ]; then
+  conda create --yes --name music_1.0.0 music=1.0.0
+fi
+if [ ! -d ${CONDA_ENVS}umitools_0.3.4 ]; then
+  conda create --yes --name umitools_0.3.4 umitools=0.3.4
+fi
+if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
+  conda create --yes --name fastp_0.19.7 fastp=0.19.7
+fi
+if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
+  conda create --yes --name gatk_3.8 gatk=3.8
+fi
+if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
+  conda create --yes --name cutadapt_1.14 cutadapt=1.14
+fi
+if [ ! -d ${CONDA_ENVS}bioawk_1.0 ]; then
+  conda create --yes --name bioawk_1.0 bioawk=1.0
+fi
+if [ ! -d ${CONDA_ENVS}canu_1.7 ]; then
+  conda create --yes --name canu_1.7 canu=1.7
+fi
+if [ ! -d ${CONDA_ENVS}fastqc_0.11.5 ]; then
+  conda create --yes --name fastqc_0.11.5 fastqc=0.11.5
+fi
+if [ ! -d ${CONDA_ENVS}bedtools_2.25.0 ]; then
+  conda create --yes --name bedtools_2.25.0 bedtools=2.25.0
+fi
+if [ ! -d ${CONDA_ENVS}macs2_2.1.2 ]; then
+  conda create --yes --name macs2_2.1.2 macs2=2.1.2
+fi
+if [ ! -d ${CONDA_ENVS}bcftools_1.7 ]; then
+  conda create --yes --name bcftools_1.7 bcftools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}salmon_0.8.2 ]; then
+  conda create --yes --name salmon_0.8.2 salmon=0.8.2
+fi
+if [ ! -d ${CONDA_ENVS}urqt_d62c1f8 ]; then
+  conda create --yes --name urqt_d62c1f8 urqt=d62c1f8
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_0.9 ]; then
+  conda create --yes --name multiqc_0.9 multiqc=0.9
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.7 ]; then
+  conda create --yes --name multiqc_1.7 multiqc=1.7
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.0 ]; then
+  conda create --yes --name multiqc_1.0 multiqc=1.0
+fi
+if [ ! -d ${CONDA_ENVS}cdhit_4.6.8 ]; then
+  conda create --yes --name cdhit_4.6.8 cdhit=4.6.8
+fi
+if [ ! -d ${CONDA_ENVS}deeptools_3.0.2 ]; then
+  conda create --yes --name deeptools_3.0.2 deeptools=3.0.2
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.9.1 ]; then
+  conda create --yes --name htseq_0.9.1 htseq=0.9.1
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.11.2 ]; then
+  conda create --yes --name htseq_0.11.2 htseq=0.11.2
+fi
+if [ ! -d ${CONDA_ENVS}R_3.4.3 ]; then
+  conda create --yes --name R_3.4.3 R=3.4.3
+fi
+if [ ! -d ${CONDA_ENVS}R_3.3.1 ]; then
+  conda create --yes --name R_3.3.1 R=3.3.1
+fi
+if [ ! -d ${CONDA_ENVS}file_handle_0.1.1 ]; then
+  conda create --yes --name file_handle_0.1.1 file_handle=0.1.1
+fi
+if [ ! -d ${CONDA_ENVS}ncdu_1.13 ]; then
+  conda create --yes --name ncdu_1.13 ncdu=1.13
+fi
+if [ ! -d ${CONDA_ENVS}picard_2.18.11 ]; then
+  conda create --yes --name picard_2.18.11 picard=2.18.11
+fi
+if [ ! -d ${CONDA_ENVS}sambamba_0.6.7 ]; then
+  conda create --yes --name sambamba_0.6.7 sambamba=0.6.7
+fi
+if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
+  conda create --yes --name star_2.7.3a star=2.7.3a
+fi
+if [ ! -d ${CONDA_ENVS}liftover_357 ]; then
+  conda create --yes --name liftover_357 ucsc-liftover==357
+fi
+if [ ! -d ${CONDA_ENVS}axtchain_377 ]; then
+  conda create --yes --name axtchain_377 ucsc-axtchain==377
+fi
+if [ ! -d ${CONDA_ENVS}ribotish_0.2.4 ]; then
+  conda create --name ribotish_0.2.4 ribotish=0.2.4
+fi

src/.conda_psmn.sh

+/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file

src/.docker_modules/bcftools/1.7/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV BCFTOOLS_VERSION=1.7
+ENV PACKAGES bcftools=${BCFTOOLS_VERSION}*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/bcftools/1.7/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bcftools:1.7
+docker build src/.docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
+docker push lbmc/bcftools:1.7

src/.docker_modules/bedtools/2.25.0/Dockerfile

+FROM ubuntu:16.04
+MAINTAINER Laurent Modolo
+
+ENV BEDTOOLS_VERSION=2.25.0
+ENV PACKAGES bedtools=${BEDTOOLS_VERSION}*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/bedtools/2.25.0/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bedtools:2.25.0
+docker build src/.docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
+docker push lbmc/bedtools:2.25.0

src/.docker_modules/bioawk/1.0/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV BIOAWK_VERSION=1.0
+ENV PACKAGES git=1:2.17* \
+   build-essential=12.4* \
+   ca-certificates=20180409 \
+   zlib1g-dev=1:1.2.11* \
+   byacc
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN git clone https://github.com/lh3/bioawk.git && \
+  cd bioawk && \
+  git checkout tags/v${BIOAWK_VERSION} && \
+  make && \
+  cd .. && \
+  mv bioawk/bioawk /usr/bin/ && \
+  rm -Rf bioawk

src/.docker_modules/bioawk/1.0/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bioawk:1.0
+docker build src/.docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
+docker push lbmc/bioawk:1.0

src/.docker_modules/bowtie/1.2.2/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV BOWTIE_VERSION=1.2.2
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES bowtie=${BOWTIE_VERSION}* \
+    samtools=${SAMTOOLS_VERSION}*
+
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/bowtie/1.2.2/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bowtie:1.2.2
+docker build src/.docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
+docker push lbmc/bowtie:1.2.2

src/.docker_modules/bowtie2/2.3.4.1/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV BOWTIE2_VERSION=2.3.4.1
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES bowtie2=${BOWTIE2_VERSION}* \
+    samtools=${SAMTOOLS_VERSION}* \
+    perl=5.26.1*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bowtie2:2.3.4.1
+docker build src/.docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
+docker push lbmc/bowtie2:2.3.4.1

src/.docker_modules/bwa/0.7.17/Dockerfile

+FROM lbmc/sambamba:0.6.9
+MAINTAINER Laurent Modolo
+
+ENV BWA_VERSION=0.7.17
+ENV SAMBLASTER_VERSION=0.1.24
+
+ENV PACKAGES curl=7.58* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
+tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
+cd bwa-${BWA_VERSION}/ && \
+make && \
+cp bwa /usr/bin && \
+cd .. && \
+rm -R bwa-${BWA_VERSION}/
+
+RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/

src/.docker_modules/bwa/0.7.17/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bwa:0.7.17
+docker build src/.docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
+docker push lbmc/bwa:0.7.17

src/.docker_modules/canu/1.6/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV CANU_VERSION=1.6
+ENV PACKAGES canu=${CANU_VERSION}*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/canu/1.6/docker_init.sh

+#!/bin/sh
+docker pull lbmc/canu:1.6
+docker build src/.docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
+docker push lbmc/canu:1.6

src/.docker_modules/cutadapt/1.14/Dockerfile

+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV CUTADAPT_VERSION=1.14
+ENV PACKAGES bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             gcc
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}

src/.docker_modules/cutadapt/1.14/docker_init.sh

+#!/bin/sh
+docker pull lbmc/cutadapt:1.14
+docker build src/.docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
+docker push lbmc/cutadapt:1.14