rnaseq-pipeline | seq pipeline for raw sequence alignment | Genomics library

 by   PavlidisLab Python Version: v2.1.4 License: Unlicense

kandi X-RAY | rnaseq-pipeline Summary

kandi X-RAY | rnaseq-pipeline Summary

rnaseq-pipeline is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. rnaseq-pipeline has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
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            kandi-support Support

              rnaseq-pipeline has a low active ecosystem.
              It has 12 star(s) with 2 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 33 open issues and 35 have been closed. On average issues are closed in 97 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of rnaseq-pipeline is v2.1.4

            kandi-Quality Quality

              rnaseq-pipeline has 0 bugs and 0 code smells.

            kandi-Security Security

              rnaseq-pipeline has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              rnaseq-pipeline code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              rnaseq-pipeline is licensed under the Unlicense License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              rnaseq-pipeline releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              It has 4812 lines of code, 160 functions and 30 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed rnaseq-pipeline and discovered the below as its top functions. This is intended to give you an instant insight into rnaseq-pipeline implemented functionality, and help decide if they suit your requirements.
            • Render the experiment summary
            • Construct a RequestsBatchInfo object
            • Yield samples from the GEO experiment
            • Query the API
            • Retrieve the samples for a given experiment
            • Count quantifications for a given experiment
            • Decorator for max retries
            • Generate a report for a given experiment
            • Complete the task
            • Returns the information for this experiment
            • Retrieve datasets for a given experiment
            • Submit experiment info to GEMMA
            • Return arguments for GEMMACLI
            • Arguments for subcommand
            • Run sratoolkit
            • Get NCBI public directory
            • Returns the output directory for the NCBI
            • Run the NCBI
            • Output the family
            • Run NCBI
            • Return a local target
            • Download the fastq file
            • Returns the output directory for the array
            • Check if the dataset exists
            • Check if this dataset exists
            • Retrieve the spreadsheet
            Get all kandi verified functions for this library.

            rnaseq-pipeline Key Features

            No Key Features are available at this moment for rnaseq-pipeline.

            rnaseq-pipeline Examples and Code Snippets

            No Code Snippets are available at this moment for rnaseq-pipeline.

            Community Discussions

            QUESTION

            Jupyter Notebook in customised docker image is not launching
            Asked 2019-May-29 at 09:44

            I have prepared the customised docker image with base image as jupyter/scipy-notebook. But after successfully building the docker image, when I am trying to run it then jupyter is not launching. I have attached the screenshot. I am not able to figure out what is missing and why. I have used norebook.sh to launch jupyter notebook. Codes are shown below:

            #!/bin/bash' # Strict mode ``set -euo pipefail

            IFS=$'\n\t'

            # Set configuration defaults : ${PASSWORD:=""} : ${PEM_FILE:="/key.pem"} : ${USE_HTTP:=0}

            HASH=$(python -c "from IPython.lib import passwd; print(passwd('${PASSWORD}'))") unset PASSWORD

            if [ $USE_HTTP -ne 0 ]; then CERTFILE_OPTION="" else if [ ! -f $PEM_FILE ]; then openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout $PEM_FILE -out $PEM_FILE \ -subj "/C=XX/ST=XX/L=XX/O=dockergenerated/CN=dockergenerated" fi

            CERTFILE_OPTION="--certfile=$PEM_FILE" fi

            jupyter notebook \ --port 8888 \ --ip=0.0.0.0 \ $CERTFILE_OPTION \ --NotebookApp.password="$HASH" \ --allow-root unset HASH

            I have taken this script from mayanlab/zika and made some changes as this script use very old versions of jupyter. I also tried with the IP address shown in screenshot as 127.0.0.1:8888 and localhost:8888 but nothing works. Kindly suggest.

            .

            ...

            ANSWER

            Answered 2019-May-29 at 09:44

            You are running the container on the host port 8887 (last command), so try http://127.0.0.1:8887 in your browser.

            The Port binding syntax in django is -p host_port:container_port, see e.g. Docker Docs

            Source https://stackoverflow.com/questions/56356633

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install rnaseq-pipeline

            The pipeline automatically generate the RSEM/STAR index and all that is required is to drop the GTF annotations file and the primary assembly FASTA files under pipeline-output/genome/<reference_id> subdirectory.
            ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
            ftp://ftp.ensembl.org/pub/release-98/gtf/mus_musculus/Mus_musculus.GRCm38.98.gtf.gz
            The pipeline is build upon Bioluigi which supports dispatching external programs on a workload manager such as Slurm.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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          • HTTPS

            https://github.com/PavlidisLab/rnaseq-pipeline.git

          • CLI

            gh repo clone PavlidisLab/rnaseq-pipeline

          • sshUrl

            git@github.com:PavlidisLab/rnaseq-pipeline.git

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