rnaseq-pipeline | seq pipeline for raw sequence alignment | Genomics library
kandi X-RAY | rnaseq-pipeline Summary
kandi X-RAY | rnaseq-pipeline Summary
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
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Top functions reviewed by kandi - BETA
- 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
rnaseq-pipeline Key Features
rnaseq-pipeline Examples and Code Snippets
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Trending Discussions on rnaseq-pipeline
QUESTION
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 09:44You 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
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install rnaseq-pipeline
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.
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