Comments (2)
lcolladotor
commented on June 1, 2024
Something similar in spirit are the get_.sh scripts from https://github.com/ChristopherWilks/bamcount that Chris Wilks wrote for bamcount
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Nick-Eagles
commented on June 1, 2024
We currently have install_software.sh for this purpose, which installs required dependencies for users without access to docker. Paths to software are automatically configured with conf/command_paths_long.config, and other users implicitly access this software without special configuration by pointing to the original user's main.nf file.
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Related Issues (20)
- [JHPCE] repeated fastqc failure on trimmed paired data HOT 15
- Guide for all setups that are atypical in some way
- Develop a 1 day (max 2) workshop
- Videos documenting how to install and run SPEAQeasy + describing outputs
- Translate course and intro documentation to Spanish
- Add support for MultiQC and maybe other tools
- Add QC metrics generated by Monorail / recount3
- Adapt code to DSL2
- Create a contribution guidelines documentation
- improve storage usage, minimize duplication of FASTQ data HOT 2
- transcript quantification (Salmon/Kallisto) should use trimmed reads HOT 1
- Add support for running SPEAQeasy with one sample
- allow starting the workflow with existing read alignments (sorted BAM/CRAM files) HOT 3
- InferStrandness failure, --force_strand not supported HOT 3
- Construct `rse_tx` for rat HOT 5
- `BuildAnnotationObjects` halts with current version of R
- Add support for more executors
- Improve or clarify what's supported for custom annotation
- PullTranscriptFasta failing HOT 1
- BuildAnnotationObjects fails HOT 19
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