Merge branch 'master' of github.com:kmpf/uap-docker

uap/Dockerfile.uap.1.0.0

@@ -22,6 +22,7 @@ RUN apt-get update && apt-get install -y \
     libncurses5-dev \
     libz-dev \
     make \
+    man \
     pigz \
     python-dev \
     python-pip \
@@ -180,7 +181,7 @@ RUN make
 ENV PATH /home/uap_user/bioinformatic-tools/segemehl/segemehl_0_2_0/segemehl:$PATH
 
 ###############################################################################
-# Install tophat2 (version: )
+# Install tophat2 (version: 2.1.1)
 ###############################################################################
 
 RUN mkdir -p /home/uap_user/bioinformatic-tools/tophat2

uap/Dockerfile.uap.1.0.0-RNAseq

@@ -24,8 +24,8 @@ RUN git checkout release && \
 WORKDIR /home/uap_user/uap/example-configurations/
 
 # Run workflow 'RNAseq-data-download.yaml'
-#RUN mkdir -p /home/uap_user/uap/example-configurations/example-out/2014-Mercer_et_al_download && \
-#    uap RNAseq-data-download.yaml run-locally
+RUN mkdir -p /home/uap_user/uap/example-configurations/example-out/2014-Mercer_et_al_download && \
+    uap RNAseq-data-download.yaml run-locally
 
 # Run workflow 'download_human_gencode_release_v19.yaml'
 RUN mkdir -p /home/uap_user/uap/example-configurations/genomes/animalia/chordata/mammalia/primates/homo_sapiens/gencode && \

uap/docker-uap.README.md

@@ -0,0 +1,132 @@
+Welcome to the uap Test Container
+=================================
+
+This container is meant to be used as a hands-on experience of uap. You can find the uap code repository at https://github.com/yigbt/uap and the documentation at https://readthedocs.org/projects/uap/.
+
+If you start the container via one of the `make docker-run-*` commands, the container will get removed as you leave it. This means downloaded or processed data will be lost after logging out of the container!
+
+Installed Bioinformatic Tools
+-----------------------------
+
+The uap test container contains installations of the following tools:
+
+Tool            | Version | Path to Executable
+--------------- | ------- | ------------------
+bowtie2         | 2.2.9   | /home/uap_user/bioinformatic-tools/bowtie2/bowtie2-2.2.9/bowtie2
+bwa             | 0.7.15  | /home/uap_user/bioinformatic-tools/bwa/bwa-0.7.15/bwa
+cufflinks       | 2.2.1   | /home/uap_user/bioinformatic-tools/cufflinks/cufflinks-2.2.1.Linux_x86_64/cufflinks
+cutadapt        | current | installed with pip, executable is available anywhere
+FastQC          | 0.11.7  | /home/uap_user/bioinformatic-tools/fastqc/FastQC/fastqc
+Fastx-Toolkit   | 0.0.13  | /home/uap_user/bioinformatic-toolsfastx-toolkit/bin/*
+fetchChromSizes | current | /home/uap_user/bioinformatic-tools/fetchChromSizes/fetchChromSizes
+HTSeq           | current | installed with pip, executable is available anywhere
+MACS2           | current | installed with pip, executable is available anywhere
+picard-tools    | current | installed with repository, executable is available anywhere
+samtools        | 1.3.1   | /home/uap_user/bioinformatic-tools/samtools/samtools-1.3.1/samtools
+segemehl        | 0.2.0   | /home/uap_user/bioinformatic-tools/segemehl/segemehl_0_2_0/segemehl/segemehl.x
+tophat2         | 2.1.1   | /home/uap_user/bioinformatic-tools/tophat2/tophat-2.1.1.Linux_x86_64/tophat2
+
+These tools are required to execute the available example workflows.
+
+uap Folders
+-----------
+
+The uap installation is found at /home/uap_user/uap/.
+The subfolders are explained in the table below:
+
+Folder                  | Explanation
+----------------------- | -----------
+example-configurations/ | Configurations for example workflows
+\|_example-out          | Output of example workflows go here
+cluster/                | Cluster configuration files
+doc/                    | Documentation
+include/steps           | Available processing steps
+include/sources         | Available source steps
+include/subcommands     | Subcommand scripts
+
+
+uap Workflows
+-------------
+
+Depending on the container you started it either already contains the genomic
+and the sequencing data or it only contains the uap installation.
+
+uap.1.0.0
+*********
+
+This container contains only an installation of uap and the described bioinformatic tools. Users can start workflows that download data such as:
+
+* download_human_gencode_release_v19.yaml
+  * Downloads the human Gencode annotation v19
+  * Downloads the human Gencode long non-coding RNA gene annotation v19
+  * the downloaded files are located in `example-configurations/genomes/animalia/chordata/mammalia/primates/homo_sapiens/gencode`
+
+* index_homo_sapiens_hg19_chr21.yaml
+  * Downloads the homo sapiens chromosome sizes from UCSC
+  * Downloads the homo sapiens chromosome 21 FASTA sequence from UCSC
+  * the downloaded files are located in `example-configurations/genomes/animalia/chordata/mammalia/primates/homo_sapiens/hg19`
+  * Generates the index for bowtie2 for chromosome 21
+  * Generates the index for bwa for chromosome 21
+  * Generates the fasta index for chromosome 21
+
+* index_homo_sapiens_hg19_genome.yaml
+  * Downloads the homo sapiens chromosome sizes from UCSC
+  * Downloads the full homo sapiens chromosome set as FASTA sequences from UCSC
+  * the downloaded files are located in `example-configurations/genomes/animalia/chordata/mammalia/primates/homo_sapiens/hg19`
+  * Generates the index for bowtie2 for the full chromosome set
+  * Generates the index for bwa for the full chromosome set
+  * Generates the fasta index for the full chromosome set
+
+* index_mycoplasma_genitalium_ASM2732v1_genome.yaml
+  * Downloads the mycoplasma genitalium genome from NCBIs Genbank, these files are located in `example-configurations/genomes/bacteria/Mycoplasma_genitalium/`
+  * Generates the index for bowtie2 for that genome
+  * Generates the index for bwa for that genome
+  * Generates the index for segemehl for that genome
+  * Generates the fasta index for that genome
+
+* ChIPseq-data-download-short.yaml
+  * Downloads the ChIPseq data of H3K4me1 and H3K4me3 published in
+   "High-Resolution Profiling of Histone Methylations in the Human Genome"
+   Barski et al., Cell, 2007
+  * the downloaded files are located in `example-configurations/example-out/2007-Barski_et_al_download`
+
+* ChIPseq-data-download-full.yaml
+  * Downloads the complete ChIPseq data published in
+   "High-Resolution Profiling of Histone Methylations in the Human Genome"
+   Barski et al., Cell, 2007
+  * the downloaded files are located in `example-configurations/example-out/2007-Barski_et_al_download`
+
+* RNAseq-data-download.yaml
+  * Downloads the RNAseq and supplementary data published in
+   "Targeted sequencing for gene discovery and quantification using RNA CaptureSeq"
+   Mercer et al., Nature protocols, 2014
+  * the downloaded files are located in `example-configurations/example-out/2014-Mercer_et_al_download`
+
+uap.1.0.0-ChIPseq
+*****************
+This container contains the uap installation, the described bioinformatic tools and the data which are required for the example workflows ChIPseq-workflow-full.yaml and ChIPseq-workflow-short.yaml.
+
+
+uap.1.0.0-RNAseq
+****************
+This container contains the uap installation, the described bioinformatic tools and the data which are required for the example workflows RNAseq-workflow-full.yaml and RNAseq-workflow-short.yaml.
+
+
+User Information
+----------------
+
+You enter this container as this user:
+
+User | Password
+---- | --------
+uap  | manager
+
+
+
+uap directory: `/home/uap_user/uap`
+tools directory: `/home/uap_user/bioinformatic-tools`
+
+
+You will now be dropped out to: `/home/uap_user/`
+
+Have fun!