pegi3s/sratoolkit Docker Image Overview

pegi3s/sratoolkit

自动构建

pegi3s

SRA Toolkit ([***] docker image.

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🚀 生产环境还在裸拉官方镜像？一次故障=一次通宵

镜像简介版本下载

🚀 生产环境还在裸拉官方镜像？一次故障=一次通宵

This image belongs to a larger project called Bioinformatics Docker Images Project ([***]

(Please note that the original software licenses still apply)

This image allows the usage of the SRA Toolkit suite. Frequently used tools in this suite are:

fastq-dump: convert SRA data into fastq format.
fasterq-dump: convert SRA data into fastq format (faster than fastq-dump).
prefetch: allows command-line downloading of SRA, dbGaP, and ADSP data.
sam-dump: convert SRA data to sam format.
sra-pileup: generate pileup statistics on aligned SRA data.
vdb-config: display and modify VDB configuration information.
vdb-decrypt: decrypt non-SRA dbGaP data ("phenotype data").

Additional tools included in this suite are:

abi-dump: convert SRA data into ABI format (csfasta / qual).
illumina-dump: convert SRA data into Illumina native formats (qseq, etc.).
sff-dump: convert SRA data to sff format.
sra-stat: generate statistics about SRA data (quality distribution, etc.).
vdb-dump: output the native VDB format of SRA data.
vdb-encrypt: encrypt non-SRA dbGaP data ("phenotype data").
vdb-validate: validate the integrity of downloaded SRA data.

To obtain the help of an application, you just need to run: docker run --rm pegi3s/sratoolkit <sratoolkit-application-name> --help (e.g. docker run --rm pegi3s/sratoolkit fastq-dump --help)

Using the SRA Toolkit image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/sratoolkit <sratoolkit-application-name> /data/mydata.sra --outdir /data/outdir

In this command, you should replace:

/your/data/dir to point to the directory that contains the SRA file you want to convert into a FASTQ file.
<sratoolkit-application-name> to the name of the SRA Toolkit application you want to use.
mydata.sra to the actual name of your input file.
outdir to the actual name of your output directory.

For instance, to download data SRR6175516 using the fastq-dump application, you should run: docker run --rm -v /your/data/dir:/data pegi3s/sratoolkit fastq-dump SRR6175516 --outdir /data

Note: Depending on DNS restrictions from your firewall institution, you may obtain an error message:

fastq-dump.3.0.1 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to '[***]

In order to solve it, you need to change your DNS Address. Please follow the steps provided here.

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pegi3s/sratoolkit

自动构建

pegi3s

SRA Toolkit ([***] docker image.

1 收藏0 次下载

🚀 生产环境还在裸拉官方镜像？一次故障=一次通宵

镜像简介版本下载

🚀 生产环境还在裸拉官方镜像？一次故障=一次通宵

This image belongs to a larger project called Bioinformatics Docker Images Project ([***]

(Please note that the original software licenses still apply)

This image allows the usage of the SRA Toolkit suite. Frequently used tools in this suite are:

fastq-dump: convert SRA data into fastq format.
fasterq-dump: convert SRA data into fastq format (faster than fastq-dump).
prefetch: allows command-line downloading of SRA, dbGaP, and ADSP data.
sam-dump: convert SRA data to sam format.
sra-pileup: generate pileup statistics on aligned SRA data.
vdb-config: display and modify VDB configuration information.
vdb-decrypt: decrypt non-SRA dbGaP data ("phenotype data").

Additional tools included in this suite are:

abi-dump: convert SRA data into ABI format (csfasta / qual).
illumina-dump: convert SRA data into Illumina native formats (qseq, etc.).
sff-dump: convert SRA data to sff format.
sra-stat: generate statistics about SRA data (quality distribution, etc.).
vdb-dump: output the native VDB format of SRA data.
vdb-encrypt: encrypt non-SRA dbGaP data ("phenotype data").
vdb-validate: validate the integrity of downloaded SRA data.

To obtain the help of an application, you just need to run: docker run --rm pegi3s/sratoolkit <sratoolkit-application-name> --help (e.g. docker run --rm pegi3s/sratoolkit fastq-dump --help)