Directory /shared/opt¶
Warnings¶
The following subdirectories are missing a README.yaml file:
- /shared/opt/cafe5
- /shared/opt/fastqc-0.12.1
- /shared/opt/gromacs-2022.6
- /shared/opt/ncbi-blast-2.7.1+
Summary¶
Found 30 README.yaml files in the directories under /shared/opt.
A summary of the metadata in these files follows.
| Directory | Title | Description | Data Manager |
|---|---|---|---|
| /shared/opt/bcl2fastq2-2.20.0 | bcl2fastq2 | Genomics software installed for Holly Pearson, Feb 2022. | Mike Lake |
| /shared/opt/beast-2.7.3 | BEAST v2.7.3 2022 | Bayesian inference using MCMC of molecular sequences. | Mike Lake |
| /shared/opt/cellranger-7.1.0 | Cellranger 7.1.0 | Genomics software installed for Holly Pearson, Feb 2022. | Mike Lake |
| /shared/opt/cellranger-arc-2.0.2 | Cellranger-arc 2.0.2 | Genomics software installed for Holly Pearson, Feb 2022. | Mike Lake |
| /shared/opt/cellranger-atac-2.1.0 | Cellranger-atac 2.1.0 | Genomics software installed for Holly Pearson, April 2022. | Mike Lake |
| /shared/opt/centos6 | Old Centos 6 programs | Older programs compiled under Centos 6. They may work under Centos 8. | Mike Lake |
| /shared/opt/fastqc-0.10.1 | FastQC | FastQC reads a set of sequence files and produces from each one a quality control report. | Mike Lake |
| /shared/opt/fastqc-0.11.9 | FastQC | FastQC reads a set of sequence files and produces from each one a quality control report. | Mike Lake |
| /shared/opt/fragpipe_21.1 | Fragpipe | A complete proteomics pipeline with the MSFragger search engine. | Mike Lake |
| /shared/opt/gromacs-2018.8 | GROMACS 2018.8 | Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Compiled with PBS MPI. | Mike Lake |
| /shared/opt/gromacs-2019.6 | GROMACS 2019.6 | Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Compiled with PBS MPI. | Mike Lake |
| /shared/opt/gromacs-2020.4 | GROMACS 2020.4 | Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Compiled with PBS MPI. | Mike Lake |
| /shared/opt/gromacs-2021.4 | GROMACS 2021.4 | Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. | Mike Lake |
| /shared/opt/intel | Intel Compiler | Intel compiler version 2018 | Mike Lake |
| /shared/opt/julia-1.0.0 | Julia Language 1.0 | High performance language for scientific applications. | Mike Lake |
| /shared/opt/julia-1.6.2 | Julia Language 1.6 | High performance language for scientific applications. | Mike Lake |
| /shared/opt/mmseqs2-v12 | MMseqs2 | Short for Many-against-Many sequence searching. MMseqs2 is an ultra fast and sensitive sequence search and clustering suite. See https://github.com/soedinglab/MMseqs2 | Mike Lake |
| /shared/opt/ncbi-blast-2.13.0+ | BLAST+ | Basic Local Alignment Search Tool | Mike Lake |
| /shared/opt/ncbi-blast-2.15.0+ | BLAST+ | Basic Local Alignment Search Tool | Mike Lake |
| /shared/opt/ncbi-blast-2.2.22+ | BLAST+ | Basic Local Alignment Search Tool | Mike Lake |
| /shared/opt/ncbi-blast-2.2.22_legacy | BLAST Legacy | Basic Local Alignment Search Tool | Mike Lake |
| /shared/opt/ncbi-blast-2.2.26_legacy | BLAST Legacy | Basic Local Alignment Search Tool | Mike Lake |
| /shared/opt/openmpi-4.0.4 | Open Message Passing Interface | Open MPI is used to compile and build parallel processing code. | Mike Lake |
| /shared/opt/openmpi-4.1.2 | Open Message Passing Interface | Open MPI is used to compile and build parallel or distributed processing code. | Mike Lake |
| /shared/opt/openmpi-4.1.5 | Open Message Passing Interface | Open MPI is used to compile and build parallel or distributed processing code. | Mike Lake |
| /shared/opt/pblat-cluster-1.1 | pblat-cluster | pblat is like BLAST but with parallel computing support. | Mike Lake |
| /shared/opt/qiime-2023.5 | QIIME 2023.5 | QIIME from https://qiime2.org. This is an apptainer image containing the software. | Mike Lake |
| /shared/opt/qristal | Qristal | Testing. From https://quantumbrilliance.com/quantum-brilliance-qristal | Mike Lake |
| /shared/opt/rh | Deprecated Redhat Packages | Older and now deprecated Redhat packages. | Mike Lake |
| /shared/opt/singularity-3.10.3 | Singularity 3.10 | Installed for Sobia Idrees in Dec 2022 as cwltool checks for this. | Mike Lake |
Metadata Information¶
The following are all the 3 metadata attributes found in the README.yaml files at this level. These should all be unique. If not edit and correct the README.yaml files.
- Data Manager
- Description
- Title
Checking each README.yaml file against the metadata list above … passed OK.
Checking each README.yaml file for disallowed characters … passed OK.
Created by DDC version 1.3.0.
This page was updated on Sat, 22 Feb 2025 at 10:10 PM