Changing name to PM4NGS

README.md

@@ -1,7 +1,7 @@
-Cookiecutter based Jupyter Notebook Templates for NGS data analysis
-============================================================
+PM4NGS: Program manager for NGS data analysis
+=============================================
 
-cookiecutter-jupyter-ngs is designed to generate a standard organizational structure for Next-generation Sequencing
+PM4NGS is designed to generate a standard organizational structure for Next-generation Sequencing
 data analysis including a directory structure for the project, Jupyter notebooks for data management and CWL workflows
 for pipeline execution.
 
@@ -14,12 +14,12 @@ define a standard files and directories for the project. The second part are **J
 interfaces for data management and visualization. The third part are the **CWL workflows** that execute the data
 analysis.
 
-**cookiecutter-jupyter-ngs** source code includes the templates used by **cookiecutter** to generate the project
+**PM4NGS** source code includes the templates used by **cookiecutter** to generate the project
 organizational structure and the Jupyter notebooks. The CWL workflows are defined in a separate GitHub project named:
 [cwl-ngs-workflows-cbb](https://github.com/ncbi/cwl-ngs-workflows-cbb).
 
 All type of projects generated from these templates follow the same design principles explained in the
-[Background Information](https://cookiecutter-jupyter-ngs.readthedocs.io/en/latest/background_information.html).
+[Background Information](https://pm4ngs.readthedocs.io/en/latest/background_information.html).
 
 Powered by [Cookiecutter](https://github.com/audreyr/cookiecutter), 
 [Jupyter Notebook](https://jupyter.org/), [CWL](https://www.commonwl.org/), [Docker](https://www.docker.com), 
@@ -28,7 +28,7 @@ Powered by [Cookiecutter](https://github.com/audreyr/cookiecutter),
 Documentation
 -------------
 
-Go to https://cookiecutter-jupyter-ngs.readthedocs.io for more detail information.
+Go to https://pm4ngs.readthedocs.io for more detail information.
 
 Reference
 ---------

docker/Dockerfile-RNASeq-DGA

@@ -8,7 +8,7 @@ LABEL software="rnaseq-dga"
 LABEL software.version="0.0.1"
 LABEL description=""
 LABEL tags="RNASeq"
-LABEL website="https://github.com/ncbi/cookiecutter-jupyter-ngs"
+LABEL website="https://github.com/ncbi/pm4ngs"
 
 # Maintainer
 MAINTAINER Roberto Vera Alvarez <veraalva@ncbi.nlm.nih.gov>

docker/Dockerfile-RNASeq-DGA-Jupyter

@@ -43,8 +43,8 @@ ENV LANGUAGE=en_US.UTF-8
 ENV LC_ALL=en_US.UTF-8
 ENV LANG=en_US.UTF-8
 
-ENV URL=https://github.com/ncbi/cookiecutter-jupyter-ngs
-ENV COOKIECUTTER_JUPYTER_NGS=/home/ubuntu/cookiecutter-jupyter-ngs
+ENV URL=https://github.com/ncbi/pm4ngs
+ENV COOKIECUTTER_JUPYTER_NGS=/home/ubuntu/pm4ngs
 
 RUN cd /home/ubuntu/ && \
         git clone --single-branch --branch develop $URL && \

docker/README.md

@@ -10,7 +10,7 @@ Image build
 Download from this folder the Dockerfile for the pipeline you're going to use. The examples are for the 
 Dockerfile-RNASeq-DGA pipeline.
 
-    docker build -t jupyter-rnaseq-pipeline https://raw.githubusercontent.com/ncbi/cookiecutter-jupyter-ngs/master/docker/Dockerfile-RNASeq-DGA
+    docker build -t jupyter-rnaseq-pipeline https://raw.githubusercontent.com/ncbi/pm4ngs/master/docker/Dockerfile-RNASeq-DGA
 
 Initialization of the data structure
 ------------------------------------

docker/aws/transannot/Dockerfile

@@ -8,7 +8,7 @@ LABEL software="transcriptome-annotation"
 LABEL software.version="0.0.1"
 LABEL description=""
 LABEL tags="transcriptome"
-LABEL website="https://github.com/ncbi/cookiecutter-jupyter-ngs"
+LABEL website="https://github.com/ncbi/pm4ngs"
 
 # Maintainer
 MAINTAINER Roberto Vera Alvarez <veraalva@ncbi.nlm.nih.gov>

docker/aws/transannot/job-definition.json

@@ -0,0 +1,57 @@
+{
+    "jobDefinitionName": "cbb-research-dl-transannot-job",
+    "jobDefinitionArn": "arn:aws:batch:us-east-1:250813660784:job-definition/cbb-research-dl-transannot-job:4",
+    "revision": 4,
+    "status": "ACTIVE",
+    "type": "container",
+    "parameters": {},
+    "containerProperties": {
+        "image": "250813660784.dkr.ecr.us-east-1.amazonaws.com/cbb-research-dl-transannot:0.0.1",
+        "vcpus": 64,
+        "memory": 252000,
+        "command": [
+            "/usr/bin/pipeline.sh"
+        ],
+        "jobRoleArn": "arn:aws:iam::250813660784:role/cbb-research-db-batch-role",
+        "volumes": [
+            {
+                "host": {
+                    "sourcePath": "/data"
+                },
+                "name": "data"
+            }
+        ],
+        "environment": [
+            {
+                "name": "AWS_ACCESS_KEY_ID",
+                "value": ""
+            },
+            {
+                "name": "BATCH_S3_BUCKET_SAMPLE",
+                "value": "cbb-research-dl-transannot"
+            },
+            {
+                "name": "AWS_SECRET_ACCESS_KEY",
+                "value": ""
+            },
+            {
+                "name": "CPU",
+                "value": "64"
+            },
+            {
+                "name": "BATCH_S3_BUCKET_CDD",
+                "value": "cbb-research-dl-transannot"
+            }
+        ],
+        "mountPoints": [
+            {
+                "containerPath": "/data",
+                "sourceVolume": "data"
+            }
+        ],
+        "privileged": true,
+        "ulimits": [],
+        "user": "nobody",
+        "resourceRequirements": []
+    }
+}

docker/gcp/rnaseq/script.sh

@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+
+gcloud beta lifesciences pipelines run --machine-type n1-standard-8  --boot-disk-size 50 \
+--command-line 'cwltool --no-container --on-error continue --outdir /gcloud-shared/ https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/master/workflows/Alignments/star-alignment-PE.cwl --threads 8 --genomeDir ${INDEX} --reads_1 ${R1} --reads_2 ${R2}' \
+--docker-image 'gcr.io/cbb-research-dl/rnaseq-dga' \
+--logging gs://cbb-research-dl-life-sciences/SRR2126795_sorted.log \
+--inputs I1=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/Genome \
+--inputs I2=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/SA \
+--inputs I3=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/SAindex \
+--inputs I4=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/chrLength.txt \
+--inputs I5=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/chrName.txt \
+--inputs I6=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/chrNameLength.txt \
+--inputs I7=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/chrStart.txt \
+--inputs I8=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/exonGeTrInfo.tab \
+--inputs I9=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/exonInfo.tab \
+--inputs I10=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/geneInfo.tab \
+--inputs I11=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/genes.gtf \
+--inputs I12=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/genome.fa \
+--inputs I13=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/genomeParameters.txt \
+--inputs I14=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/sjdbInfo.txt \
+--inputs I15=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/sjdbList.fromGTF.out.tab \
+--inputs I16=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/sjdbList.out.tab \
+--inputs I17=gs://ngs-resources/indexes/STAR-2.7.1a/hg38/transcriptInfo.tab \
+--inputs R1=gs://cbb-research-dl-life-sciences/SRR2126795_1.fastq.gz \
+--inputs R2=gs://cbb-research-dl-life-sciences/SRR2126795_2.fastq.gz \
+--outputs BAM=gs://cbb-research-dl-life-sciences/SRR2126795_sorted.bam \
+--outputs BAI=gs://cbb-research-dl-life-sciences/SRR2126795_sorted.bam.bai \
+--outputs STATS=gs://cbb-research-dl-life-sciences/SRR2126795Aligned.out.stats \
+--outputs LOG=gs://cbb-research-dl-life-sciences/SRR2126795Log.final.out \
+--outputs READS=gs://cbb-research-dl-life-sciences/SRR2126795ReadsPerGene.out.tab \
+--env-vars=INDEX=/gcloud-shared/,\
+R1=/gcloud-shared/SRR2126795_1.fastq.gz,\
+R2=/gcloud-shared/SRR2126795_2.fastq.gz,\
+I1=/gcloud-shared/Genome,\
+I2=/gcloud-shared/SA,\
+I3=/gcloud-shared/SAindex,\
+I4=/gcloud-shared/chrLength.txt,\
+I5=/gcloud-shared/chrName.txt,\
+I6=/gcloud-shared/chrNameLength.txt,\
+I7=/gcloud-shared/chrStart.txt,\
+I8=/gcloud-shared/exonGeTrInfo.tab,\
+I9=/gcloud-shared/exonInfo.tab,\
+I10=/gcloud-shared/geneInfo.tab,\
+I11=/gcloud-shared/genes.gtf,\
+I12=/gcloud-shared/genome.fa,\
+I13=/gcloud-shared/genomeParameters.txt,\
+I14=/gcloud-shared/sjdbInfo.txt,\
+I15=/gcloud-shared/sjdbList.fromGTF.out.tab,\
+I16=/gcloud-shared/sjdbList.out.tab,\
+I17=/gcloud-shared/transcriptInfo.tab,\
+BAM=/gcloud-shared/SRR2126795_sorted.bam,\
+BAI=/gcloud-shared/SRR2126795_sorted.bam.bai,\
+STATS=/gcloud-shared/SRR2126795Aligned.out.stats,\
+LOG=/gcloud-shared/SRR2126795Log.final.out,\
+READS=/gcloud-shared/SRR2126795ReadsPerGene.out.tab

docker/gcp/transannot/Dockerfile

@@ -8,7 +8,7 @@ LABEL software="transcriptome-annotation"
 LABEL software.version="0.0.1"
 LABEL description=""
 LABEL tags="transcriptome"
-LABEL website="https://github.com/ncbi/cookiecutter-jupyter-ngs"
+LABEL website="https://github.com/ncbi/pm4ngs"
 
 # Maintainer
 MAINTAINER Roberto Vera Alvarez <veraalva@ncbi.nlm.nih.gov>

docs/source/background_information.rst

@@ -4,7 +4,7 @@ Background Information
 Project organizational structure
 --------------------------------
 
-**cookiecutter-jupyter-ngs** creates, from a configuration yaml file, a project organizational structure that allows
+**pm4ngs** creates, from a configuration yaml file, a project organizational structure that allows
 users organize the relevant files and directories in a standard way. The main idea behind this organizational
 structure is allow someone unfamiliar with the project understand how the data analysis process was executed and an
 easy localization of any file inside the project directories.

docs/source/conf.py

@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'cookiecutter-jupyter-ngs'
+project = 'pm4ngs'
 copyright = '2019, National Center for Biotechnology Information, NLM/NIH'
 author = 'Roberto Vera Alvarez'
 

docs/source/cwl/meme-motif.rst

@@ -69,4 +69,4 @@ The downloaded files should be uncompressed in a directory **data/meme**. The fi
 
     19 directories
 
-See also an example in our test project: https://ftp.ncbi.nlm.nih.gov/pub/cookiecutter-jupyter-ngs/examples/chipexo-single/data/
+See also an example in our test project: https://ftp.ncbi.nlm.nih.gov/pub/pm4ngs/examples/chipexo-single/data/

docs/source/envs/installation.rst

@@ -10,7 +10,7 @@ Install Cookiecutter and other basic Python packages using the **requirements.tx
 
     localhost:~> virtualenv venv-templates
     localhost:~> source venv-templates/bin/activate
-    localhost:~> pip install -r https://raw.githubusercontent.com/ncbi/cookiecutter-jupyter-ngs/master/requirements.txt
+    localhost:~> pip install -r https://raw.githubusercontent.com/ncbi/pm4ngs/master/requirements.txt
 
 
 Project Templates with Conda/BioConda
@@ -27,7 +27,7 @@ A Conda virtual environment will be created with name **templates** using these
 
 .. code-block:: bash
 
-    localhost:~> wget https://raw.githubusercontent.com/ncbi/cookiecutter-jupyter-ngs/master/conda-requirements.yaml
+    localhost:~> wget https://raw.githubusercontent.com/ncbi/pm4ngs/master/conda-requirements.yaml
     localhost:~> conda env create -f conda-requirements.yaml
 
 If Conda is installed with prefix **/gfs/conda** you should see the available environments like in this block:

docs/source/envs/jupyter_env.rst

@@ -32,7 +32,7 @@ these commands:
 
 .. code-block:: bash
 
-    localhost:~> wget https://raw.githubusercontent.com/ncbi/cookiecutter-jupyter-ngs/master/%7B%7Bcookiecutter.project_name%7D%7D/requirements/python.txt
+    localhost:~> wget https://raw.githubusercontent.com/ncbi/pm4ngs/master/%7B%7Bcookiecutter.project_name%7D%7D/requirements/python.txt
     localhost:~> virtualenv -p `which python3` venv
     localhost:~> source venv/bin/activate
     localhost:~> pip install -r python.txt
@@ -46,4 +46,4 @@ For using the Python virtual environment
 
     localhost:~> source venv/bin/activate
 
-.. _requirements: https://raw.githubusercontent.com/ncbi/cookiecutter-jupyter-ngs/master/%7B%7Bcookiecutter.project_name%7D%7D/requirements/python.txt
+.. _requirements: https://raw.githubusercontent.com/ncbi/pm4ngs/master/%7B%7Bcookiecutter.project_name%7D%7D/requirements/python.txt

docs/source/index.rst

@@ -1,7 +1,7 @@
-cookiecutter-jupyter-ngs
+PM4NGS
 ===================================================================
 
-`cookiecutter-jupyter-ngs`_ was designed to generate a standard organizational structure for Next Generation Sequencing
+`PM4NGS`_ was designed to generate a standard organizational structure for Next Generation Sequencing
 (ngs) data analysis. It includes a directory structure for the project, several Jupyter notebooks for data management
 and  CWL workflows for pipeline execution.
 
@@ -15,14 +15,14 @@ The project is composed of three main parts.
 #. Jupyter Notebooks as user interfaces for data management and visualization
 #. CWL workflows that execute the data analysis
 
-**cookiecutter-jupyter-ngs** source code includes the templates used by **cookiecutter** to generate the project
+**PM4NGS** source code includes the templates used by **cookiecutter** to generate the project
 organizational structure and the Jupyter notebooks. The CWL workflows are defined in a separate GitHub project named:
 `cwl-ngs-workflows-cbb`_.
 
 All projects generated from these templates follow the same design principles explained in the
 :doc:`Background Information </background_information>`.
 
-.. _cookiecutter-jupyter-ngs: https://github.com/ncbi/cookiecutter-jupyter-ngs
+.. _PM4NGS: https://github.com/ncbi/pm4ngs
 .. _A Quick Guide to Organizing Computational Biology Projects: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424
 .. _GNU Parallel: https://www.gnu.org/software/parallel/
 .. _cwl-ngs-workflows-cbb: https://github.com/ncbi/cwl-ngs-workflows-cbb

docs/source/workflows/det_bind_chipexo.rst

@@ -69,7 +69,7 @@ following output.
 
 .. code-block:: bash
 
-    localhost:~> cookiecutter --no-input --config-file chipexo-single.yaml https://github.com/ncbi/cookiecutter-jupyter-ngs.git
+    localhost:~> cookiecutter --no-input --config-file chipexo-single.yaml https://github.com/ncbi/pm4ngs.git
     Checking ChIP-exo workflow dependencies .......... Done
     localhost:~>
 
@@ -235,7 +235,7 @@ following output.
 
 .. code-block:: bash
 
-    localhost:~> cookiecutter --no-input --config-file chipexo-single.yaml https://github.com/ncbi/cookiecutter-jupyter-ngs.git
+    localhost:~> cookiecutter --no-input --config-file chipexo-single.yaml https://github.com/ncbi/pm4ngs.git
     Checking ChIP-exo workflow dependencies .......... Done
     localhost:~>
 
@@ -332,7 +332,7 @@ CWL workflows
 Test Project
 ------------
 
-A test project is available (read-only) at https://ftp.ncbi.nlm.nih.gov/pub/cookiecutter-jupyter-ngs/examples/chipexo-single/
+A test project is available (read-only) at https://ftp.ncbi.nlm.nih.gov/pub/pm4ngs/examples/chipexo-single/
 
 Extra requirements
 ------------------

docs/source/workflows/diff_bind_event_chipseq.rst

@@ -69,7 +69,7 @@ following output.
 
 .. code-block:: bash
 
-    localhost:~> cookiecutter --no-input --config-file chipseq-hmgn1.yaml https://github.com/ncbi/cookiecutter-jupyter-ngs.git
+    localhost:~> cookiecutter --no-input --config-file chipseq-hmgn1.yaml https://github.com/ncbi/pm4ngs.git
     Checking ChIP-Seq workflow dependencies .......... Done
     localhost:~>
 
@@ -235,7 +235,7 @@ following output.
 
 .. code-block:: bash
 
-    localhost:~>  cookiecutter --no-input --config-file chipseq-paired.yaml https://github.com/ncbi/cookiecutter-jupyter-ngs.git
+    localhost:~>  cookiecutter --no-input --config-file chipseq-paired.yaml https://github.com/ncbi/pm4ngs.git
     Cloning Git repo: https://github.com/ncbi/cwl-ngs-workflows-cbb to /home/veraalva/chipseq-hmgn1/bin/cwl-ngs-workflows-cbb
     Creating a Python3.7 virtualenv
     Installing packages in: /home/veraalva/chipseq-hmgn1/venv using file /home/veraalva/chipseq-hmgn1/requirements/python.txt
@@ -362,7 +362,7 @@ CWL workflows
 Test Project
 ------------
 
-A test project is available (read-only) at https://ftp.ncbi.nlm.nih.gov/pub/cookiecutter-jupyter-ngs/examples/chipseq-hmgn1
+A test project is available (read-only) at https://ftp.ncbi.nlm.nih.gov/pub/pm4ngs/examples/chipseq-hmgn1
 
 Extra requirements
 ------------------

docs/source/workflows/diff_gene_exp_rnaseq.rst

@@ -69,7 +69,7 @@ following output.
 
 .. code-block:: bash
 
-    localhost:~> cookiecutter --no-input --config-file rnaseq-sra-paired.yaml https://github.com/ncbi/cookiecutter-jupyter-ngs.git
+    localhost:~> cookiecutter --no-input --config-file rnaseq-sra-paired.yaml https://github.com/ncbi/pm4ngs.git
     Checking RNA-Seq workflow dependencies .......... Done
     localhost:~>
 
@@ -237,7 +237,7 @@ following output.
 
 .. code-block:: bash
 
-    localhost:~> cookiecutter --no-input --config-file rnaseq-sra-paired.yaml https://github.com/ncbi/cookiecutter-jupyter-ngs.git
+    localhost:~> cookiecutter --no-input --config-file rnaseq-sra-paired.yaml https://github.com/ncbi/pm4ngs.git
     Cloning Git repo: https://github.com/ncbi/cwl-ngs-workflows-cbb to /home/veraalva/rnaseq-sra-paired/bin/cwl-ngs-workflows-cbb
     Creating a Python3.7 virtualenv
     Installing packages in: /home/veraalva/rnaseq-sra-paired/venv using file /home/veraalva/rnaseq-sra-paired/requirements/python.txt
@@ -358,7 +358,7 @@ CWL workflows
 Test Project
 ------------
 
-A test project is available (read-only) at https://ftp.ncbi.nlm.nih.gov/pub/cookiecutter-jupyter-ngs/examples/rnaseq-sra-paired
+A test project is available (read-only) at https://ftp.ncbi.nlm.nih.gov/pub/pm4ngs/examples/rnaseq-sra-paired
 
 Extra requirements
 ------------------