Mercurial > repos > richard-burhans > ncbi_egapx

annotate test-data/input.yaml @ 5:bf80a7ed8595 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
author richard-burhans
date Tue, 10 Sep 2024 21:11:47 +0000
parents 4420dd857c41
children 5bec47dfe99a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
1 # This is a very minimal example of EGAPx, it fits into 4 CPU cores and 6GB of memory.
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
2 # To be able to do this, we culled the input files and some stages of execution.
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
3 # To limit the requirements you also need to use -e docker_minimal
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
4
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
5 genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
6 reads:
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
7 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
8 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
9 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
10 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
11 taxid: 6954
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
12 proteins: []
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
13 hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
14 tasks:
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
15 star_wnode:
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
16 star_wnode: -cpus-per-worker 4
4420dd857c41 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 050f870384e004445d3dcfb56302b7894793bd23
richard-burhans
parents: 0
diff changeset
17