jhuanglab / bioinstaller Goto Github PK

Configuration file: github.toml
Description: VariantTools, software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis.

[varianttools]
github_url = "https://github.com/vatlab/VariantTools"
install = "pip install ."

Configuration file: github.toml
Description: "This Snakemake pipeline implements the GATK best-practices workflow"

[snakemake_dna_gatk_flow]
github_url = "https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling"

• Add tag of softwares and databases in inst/extdata/tag.toml to found softwares more easily (BWA/GMAP)
• Add description of softwares and databases in inst/extdata/description.toml to get the foundmental infomation e.g. publication journal, popularity (BWA/GMAP)

Configuration file: github.toml
Description: "mRNN is an implementation of a Gated Recurrent Unit (GRU) network for classification of transcripts as either coding or noncoding."

[mrnn]
github_url = "https://github.com/hendrixlab/mRNN"

Hello,

We were trying to load the app in the web server after the installation of shiny and BioInstaller. We are getting the URL path for loading the page on web server, but it is not getting loaded. Please find the attachment of the error we are facing.

Any help regarding this is appreciated.

Thank you!

Configuration file: nongithub.toml
Description: HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

[hgtid]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/hgtid/{{version}}"
version_available = ["HGT-ID_v1.0.tar.gz", "sampleResults.zip"]

I guess it is better to discuss all off-topic theme in this post.

• Error: initial (@test_install_uilts.R#40)
• Failure: is.biosoftwares.db.active (@test_active.R#10)
• Failure: set.makedir (@test_install_uilts.R#60)
• Failure: set.makedir (@test_install_uilts.R#63)
• Failure: set.makedir (@test_install_uilts.R#65)

Introduction

The main aim of this forum is to provide a fully free place sharing the bioinformatics tools/scripts and databases. The resources recorded in the posts will be integrated into the BioInstaller configuration files. Please read this post when you want to submit a new post in this forum.

Allowed posts

• Any bioinformatics related papers
• Any bioinformatics related tools/scripts and databases (Both open and restricted)
• Suggestions for improving this community
• Bug report

Reference format for sharing papers

Required fields: author name., title. journal, year, project URL, tags

• Sundaram, L., et al., Predicting the clinical impact of human mutation with deep neural networks. Nat Genet, 2018. URL: https://basespace.illumina.com/s/cPgCSmecvhb4 Tags: clinical, mutation annotation

Reference format for uploading new BioInstaller item

There is three part required for uploading a new BioInstaller item:

• Configuration file: (github.toml, nongithub.toml, db_annovar.toml, db_main.toml, or new) found in here
• title: Short title
• description: Summary of the tools/scripts and databases
• publication: Publication papers information
• TOML format configuration (see here)

Demo 1:

Configuration file: github.toml
description: GATK variant calling workflow based on [snakemake] (https://snakemake.readthedocs.io/en/stable/)
publication: Not yet

[snakemake_dna_gatk_flow]
github_url = "https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling"

Demo 2:

Configuration file: nongithub.toml
description: Mirror URL of GATK4

[gatk4_jhuang_mirror]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/gatk/gatk-{{version}}.zip"
version_available = ["4.0.6.0", "4.0.0.0"]

Configuration file: db_main.toml
Description: miRDB is an online database for miRNA target prediction and functional annotations.

[db_mirdb]
source_url = "http://mirdb.org/download/miRDB_v{{version}}_prediction_result.txt.gz"
version_avaliable = ["5.0", "4.0", "3.0", "2.0", "1.0"]

Hello

How can we install tools into Bioshiny using BioInstaller? Can we install all the required tools in one go rather than downloading it separately?

Thanking in advance for the help!

Regards

Dear All,

How can we build pipeline using BioInstaller after the installation of tools/software?

Using the tools mentioned below

1. trimmomatic
2. hisat2
3. samtools
4. feature count
5. DESeq2

I am trying to build a transcriptome pipeline using BioInstaller. There are no manual/ procedure for building pipeline.

Any help regarding this would be appreciated!

Thanks & Regards
Anoopa

I will integrate the items written in this post to my Bioinformatics-Resources project.

Deep learning based

• Sundaram, L., et al., Predicting the clinical impact of human mutation with deep neural networks. Nat Genet, 2018. URL: https://basespace.illumina.com/s/cPgCSmecvhb4 Tags: clinical, mutation annotation

Blockchain technologies in genomics

• Ozercan, H.I., et al., Realizing the potential of blockchain technologies in genomics. Genome Res, 2018. doi: 10.1101/gr.207464.116. Tags: genomics, blockchain

Databases

• LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Res 2019, in press.
• PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. Nucleic Acids Res 2018

Configuration file: nongithub.toml

Description: effusion, A method for predicting protein function, Effusion, that uses a sequence similarity network to add context for homology transfer, a probabilistic model to account for the uncertainty in labels and function propagation, and the structure of the Gene Ontology (GO) to best utilize sparse input labels and make consistent output predictions. Effusion's model makes it practical to integrate rare experimental data and abundant primary sequence and sequence similarity.

Homepage: http://www.babbittlab.ucsf.edu/effusion/

Publication: Effusion: Prediction of Protein Function from Sequence Similarity Networks. Bioinformatics. 2018 Aug 01, PMID: 30084920 DOI: 10.1093/bioinformatics/bty672

[effusion]
source_url = "http://www.babbittlab.ucsf.edu/effusion/effusion_{{version}}.tar.gz"
version_available = ["1.0.0"]