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Cardinal
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
Pitzer
HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.
Pitzer
TAU Commander is a user interface for the TAU Performance System, a set of tools for analyizing the performance of parallel programs.
Pitzer
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
Ascend, Cardinal, Pitzer
Apptainer (formerly Singularity) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.
Ascend, Cardinal, Pitzer
HTSlib is a C library used for reading and writing high-throughput sequencing data.
Ascend, Pitzer
RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
We have identified some issues with the RELION installations. For more details, please refere the "Known Issues" section below.
To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.
The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.
To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.
The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.
