bioconda.github.io

Using bioconda — Bioconda documentation

Is a channel for the conda. Package manager specializing in bioinformatics software. Bioconda consists of:. A repository of recipes. That turns these recipes into conda packages. A repository of 1500 bioinformatics packages. Ready to use with. Over 130 contributors that add, modify, update and maintain the recipes. Browse packages in the bioconda channel:. Conda allows separation of packages into separate repositories, or. Bioconda supports only 64-bit Linux and Mac OSX. 2 Set up channels. After installi...

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Using bioconda — Bioconda documentation | bioconda.github.io Reviews

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Is a channel for the conda. Package manager specializing in bioinformatics software. Bioconda consists of:. A repository of recipes. That turns these recipes into conda packages. A repository of 1500 bioinformatics packages. Ready to use with. Over 130 contributors that add, modify, update and maintain the recipes. Browse packages in the bioconda channel:. Conda allows separation of packages into separate repositories, or. Bioconda supports only 64-bit Linux and Mac OSX. 2 Set up channels. After installi...

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Using bioconda — Bioconda documentation | bioconda.github.io Reviews

https://bioconda.github.io

Is a channel for the conda. Package manager specializing in bioinformatics software. Bioconda consists of:. A repository of recipes. That turns these recipes into conda packages. A repository of 1500 bioinformatics packages. Ready to use with. Over 130 contributors that add, modify, update and maintain the recipes. Browse packages in the bioconda channel:. Conda allows separation of packages into separate repositories, or. Bioconda supports only 64-bit Linux and Mac OSX. 2 Set up channels. After installi...

INTERNAL PAGES

bioconda.github.io

1

Troubleshooting failed recipes — Bioconda documentation

http://bioconda.github.io/troubleshooting.html

Reading bioconda-utils logs on Travis-CI. For successfully-built recipes, bioconda-utils will report build start/success and test start/success. If a recipe fails, an error log message starting with. Will be printed. After that will be some verbose output. That output is the captured, merged stdout and stderr from running conda-build on that recipe. Usually the easiest thing to do is grep for. Log line, likely a. At the end of the log are. HTTP 404 errors can happen if a url used for a recipe was not sta...

2

Available packages — Bioconda documentation

http://bioconda.github.io/recipes.html

Bioconductor-bsgenome.mmusculus.ucsc.mm9. Plant tribes assembly post processor. Plant tribes assembly post processor. Plant tribes assembly post processor. Plant tribes assembly post processor. Plant tribes phylogenomics analysis. 121 2015.01.08. Bioconductor-bsgenome.mmusculus.ucsc.mm10. Bioconductor-org.ce.eg.db. Bioconductor-txdb.hsapiens.ucsc.hg19.knowngene. Bioconductor-bsgenome.dmelanogaster.ucsc.dm3. Bioconductor-org.mm.eg.db. Bioconductor-org.mm.eg.db. Bioconductor-org.hs.eg.db. 01 2015 12 21.

3

FAQs — Bioconda documentation

http://bioconda.github.io/faqs.html

This section is to help contributors get up to speed on various topics related to building and testing conda packages. What’s the difference between Anaconda, conda, and Miniconda? The Anaconda Python distribution. Started out as a bundle of scientific Python packages that were otherwise difficult to install. It was created by ContinuumIO. And remains the easiest way to install the full scientific Python stack. File that defines these settings and a. On the recipe. A package is a bgzipped tar file (.

4

Contributing — Bioconda documentation

http://bioconda.github.io/contributing.html

Bioconda is completely dependent on contributors to add, update, and maintain recipes. Every little bit helps! Below are instructions for one-time setup as well as a general procedure to follow for each recipe you’d like to add. Git and GitHub (one-time setup). Install conda and Docker (one-time setup). Request to be added to the bioconda team. Update repo and requirements. Push changes, wait for tests to pass, submit pull request. Use your new recipe. Reading bioconda-utils logs on Travis-CI.

5

Contributing a recipe — Bioconda documentation

http://bioconda.github.io/contribute-a-recipe.html

The following steps are done for each recipe or batch of recipes you’d like to contribute. Update repo and requirements. Before starting, it’s best to update your fork with any changes made recently to the upstream bioconda repo. Assuming you’ve set up your fork as above. Git checkout master git pull upstream master. Simulate-travis.py - set-channel-order ./simulate-travis.py - install-requirements. Check out a new branch in your fork (here the branch is arbitrarily named “my-recipe”):. For the first time.

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lh3.github.io

Bioconda: a capable bio-software package manager

http://lh3.github.io/2015/12/07/bioconda-the-best-package-manager-so-far

Bioconda: a capable bio-software package manager. Firstly, a few basic concepts. Conda. Is a portable package manager primarily for Python and precompiled binaries. Miniconda is the base system of conda. It includes a standard python and a few required dependencies such as readline and sqlite. In conda, a. Contains a set of software typically managed by the same group. Bioconda. Is a channel of conda focusing on bioinformatics software. The following shows how to install and use conda. Thirdly, conda is ...

bcbio-nextgen.readthedocs.io

Common Workflow Language (CWL) — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/cwl.html

Common Workflow Language (CWL). Generating CWL from bcbio. Running bcbio CWL on Arvados. Running bcbio CWL on Toil. Common Workflow Language (CWL). Common Workflow Language (CWL). Bcbio has in-progress support for running with Common Workflow Language (CWL). Compatible parallelization software. bcbio generates a CWL workflow from a sample YAML description file. Compatible workflow. The actual biological code execution during runs works with either the bcbio docker container ( bcbio/bcbio. The implementat...

bcbio-nextgen.readthedocs.io

Installation — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html

Proxy or firewall problems. GATK or Java Errors. Common Workflow Language (CWL). We provide an automated script that installs third party analysis tools, required genome data and python library dependencies for running human variant and RNA-seq analysis, bundled into an isolated directory or virtual environment:. Bcbio should install cleanly on Linux systems. For Mac OSX, we suggest trying bcbio-vm. Which runs bcbio on Amazon Web Services. And tools are in. Bcbio nextgen install.py. The machine will need...

pmelsted.wordpress.com

Building Binaries for Bioinformatics | Bits of Bioinformatics

https://pmelsted.wordpress.com/2015/10/14/building-binaries-for-bioinformatics

Skip to primary content. Building Binaries for Bioinformatics. October 14, 2015. Tl;dr there is a recipe for compiling binaries at the end. I run a cluster which runs on the rocks cluster system. The newest version at the time was based on Centos6, the compiler was gcc 4.4, even old at the time. The reason is that distributions are reluctant to use the latest compilers and so users are stuck with old technologies. How bad can it be? Linux is wonderful, but it’s not the happy wonderland we would lik...

bio-info-trainee.com

基础软件 | 生信菜鸟团

http://www.bio-info-trainee.com/category/basic-bio-infomatics/basic-software

欢迎加群生信菜鸟团 201161227，或者去论坛biotrainee.com留言参与讨论. Skip to primary content. Skip to secondary content. Scalpel is available here: http:/ scalpel.sourceforge.net/. 文章是 http:/ www.nature.com/nmeth/journal/v11/n10/full/nmeth.3069.html. 软件说明书写的也比较详细 http:/ scalpel.sourceforge.net/manual.html. Continue reading →. 熟悉GSEA软件的都知道，它只需要GCT,CLS和GMT文件，其中GMT文件，GSEA的作者已经给出了一大堆就是记录broad的 Molecular Signatures Database (MSigDB). 已经收到了18026个geneset，但是我奇怪的是里面竟然没有包括cancer testis的gene set，MSigDB的确是多，但未必全，其实里面还有很多重复。教程 https:/...

qiime.org

QIIME Installation Guide — Homepage

http://qiime.org/install/install.html

News and Announcements ». Installing QIIME on Mac OS X and Linux using Miniconda. QIIME consists of native Python 2 code and additionally wraps many external applications. These instructions describe how to perform a base installation of QIIME using Miniconda. Step 1: Install Miniconda. Flag when you create a new environment; otherwise the default Python version will be Python 3. Begin by downloading Miniconda. And following the associated installation instructions. Conda create -n qiime1 python=2.7 ...

compomics.github.io

peptide-shaker - Compomics Docs

http://compomics.github.io/projects/peptide-shaker.html

Bioinformatics for Proteomics Tutorial. Vaudel et al. Nature Biotechnol. 2015 Jan;33(1):22 24. If you use PeptideShaker as part of a publication, please include this reference. V1162 - All platforms. Click on a figure to see the full size version). PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X! PeptideShaker currently supports nine different analysis tasks:. For further help see the Bioinf...

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Using bioconda — Bioconda documentation

Is a channel for the conda. Package manager specializing in bioinformatics software. Bioconda consists of:. A repository of recipes. That turns these recipes into conda packages. A repository of 1500 bioinformatics packages. Ready to use with. Over 130 contributors that add, modify, update and maintain the recipes. Browse packages in the bioconda channel:. Conda allows separation of packages into separate repositories, or. Bioconda supports only 64-bit Linux and Mac OSX. 2 Set up channels. After installi...

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