Our January newsletter includes fifteen new and updated software titles and fifteen new R packages. Spring workshop and training registrations are open for both The Harvard Chan Bioinformatics Core and HMS Research Computing.
Testing is underway with Apple's new M1 "apple silicon" ARM64 based macs. We expect to support M1 based Macs in early 2021. This may include a combination of direct support with OS11 and the Apple Rosetta compatibility environment.
New BioGrids Install Client
We have updated our command-line installation manager, "sbgrid-cli", to version 2.1.3 (2.1.4 is coming soon). This new version, available for Mac and Linux, has many improvements including multithreaded rsync transfer, selectable installation target path, and network diagnostics for troubleshooting.
For details on how to access this new version, see our wiki at https://sbgrid.org//wiki/sbgrid-cli.
Activated users can download the new version and use it without additional activation or registration steps.
As always, please let us know if you have any questions or problems upgrading - firstname.lastname@example.org
Remote Working Help
The BioGrids Wiki provides step by step instructions for installing BioGrids software on a local laptop or desktop machine. If you prefer a live demonstration, or run into trouble, please contact email@example.com. We can set up a Zoom meeting to assist you.
MacOS 10.15 Catalina
While we recommend not upgrading to 10.15 on any Mac with BioGrids already installed, we have implemented a workaround to install BioGrids and SBGrid on new machines. Two approaches are available.
If your use of BioGrids supplied software was an important element in your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
Register here to try out our software installer, which allows users to choose from over 290 bioinfomatics and life sciences tools that can be installed as ready-to-run applications on Mac or Linux machines with the click of a button or a short command from the CLI. No need to worry about dependencies or compilation.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: firstname.lastname@example.org.
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download using the link button above and register here for activation.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide 335 titles in five categories and over 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids
If you are new to BioGrids and would like to quickly get started with the command line version, follow the instructions below:
1: Download the BioGrids Installer command line version
./biogrids activate biogrid-production jvinent1 70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
Replace the site name, user name and activation key with your own credentials.
3: Install software with BioGrids
./biogrids install fastqc trimmomatic samtools star subread igv
When finished, verify applications are installed:
Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Versions: 2.1.1 | Linux 64
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
Versions: 1.0.4 | OS X INTEL 1.0.4 | Linux 64
emacs is an extensible, customizable, free/libre text editor.
Versions: 26.3 | Linux 64 26.3 | OS X INTEL
Google Cloud SDK is a set of tools and libraries for interacting with Google Cloud products and services.
Versions: 316.0.0 | OS X INTEL 316.0.0 | Linux 64
IGV (Integrative Genomics Viewer) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Versions: 2.8.13 | Linux 64 2.8.13 | OS X INTEL
Julia The Julia programming language is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Versions:1.4.2 | Linux 64 1.3.1 | Linux 64 1.4.2 | OS X INTEL 1.3.1 | OS X INTEL 1.5.3 | OS X INTEL 1.5.3 | Linux 64
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
Versions:7.475 | Linux 64 7.475 | OS X INTEL
NanoPack is a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.
Versions: 1.1.1 | Linux 64 1.1.1 | OS X INTEL
PyRQA is a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.
Versions: 7.0.1 | OS X INTEL 7.0.1 | Linux 64
Python is a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability.
Versions: 3.6.5 | Linux 64
R is a free software environment for statistical computing and graphics.
Versions: 3.6.2 | OS X INTEL
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Versions: r3.6.2-latest | Linux 64 r3.6.2-20210125 | Linux 64
scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.
Versions: 0.8.1 | Linux 64
sniffles is a structural variation caller using third generation sequencing.
Versions: 1.0.12b | Linux 64
tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
Versions: 1.5.1 | OS X INTEL 1.5.1 | Linux 64