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Merged
skchronicles merged 2 commits into from
Mar 10, 2025
Merged

Update bigsky.json #40

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fbbd771
Update bigsky.json
rroutsong Mar 10, 2025
ec70e0b
Updating remaining /gs1 bigsky paths
skchronicles Mar 10, 2025
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2 changes: 1 addition & 1 deletion config/bigsky.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"sif": "/gs1/RTS/OpenOmics/SIFs/",
"sif": "/data/openomics/SIFs/",
"mounts": {
"kaiju": {
"to": "/opt/kaiju",
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10 changes: 5 additions & 5 deletions docs/execution.md
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Expand Up @@ -12,8 +12,8 @@ The **weave** pipeline can be triggered from a head node in a non-interactive fa
## Bigsky/Skyline

!!! Note
Dependency files for skyline and bigsky differ <br />
**Bigsky: `/gs1/RTS/OpenOmics/bin/dependencies.sh`** <br />
Dependency files for skyline and bigsky are now the same <br />
**Bigsky: `/data/openomics/bin/dependencies.sh`** <br />
**Skyline: `/data/openomics/bin/dependencies.sh`**

```bash
Expand All @@ -35,8 +35,8 @@ srun --export=ALL "module load snakemake singularity; weave run [keyword args] $
## Bigsky/Skyline

!!! Note
Dependency files for skyline and bigsky differ <br />
**Bigsky: `/gs1/RTS/OpenOmics/bin/dependencies.sh`** <br />
Dependency files for skyline and bigsky are now the same <br />
**Bigsky: `/data/openomics/bin/dependencies.sh`** <br />
**Skyline: `/data/openomics/bin/dependencies.sh`**

```bash
Expand Down Expand Up @@ -114,4 +114,4 @@ Same sbatch execution as bigsky/skyline.

```bash
sbatch weave_script.sbatch
```
```
8 changes: 4 additions & 4 deletions docs/install.md
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Expand Up @@ -37,7 +37,7 @@ Biowulf uses environmental modules to control software. After executing the abov
> [+] Loading singularity 4.X.X on cnXXXX

```bash title="<b>Bigsky</b>"
source /gs1/RTS/OpenOmics/bin/dependencies.sh`
source /data/openomics/bin/dependencies.sh`
```

Bigsky uses spack to load modules so a consolidated conda environment with snakemake is activated:
Expand All @@ -50,10 +50,10 @@ if [ ! -x "$(command -v "snakemake")" ]; then
source activate snakemake7-19-1
fi
# Add this folder to $PATH
export PATH="/gs1/RTS/OpenOmics/bin:${PATH}"
export PATH="/data/openomics/bin:${PATH}"
# Add different pipelines to $PATH
export PATH="/gs1/RTS/OpenOmics/prod/rna-seek/latest:${PATH}"
export PATH="/gs1/RTS/OpenOmics/prod/metavirs/latest:${PATH}"
export PATH="/data/openomics/prod/rna-seek/latest:${PATH}"
export PATH="/data/openomics/prod/metavirs/latest:${PATH}"
```

While, singularity is installed to the **BigSky** system and available upon login.
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2 changes: 1 addition & 1 deletion docs/usage/run.md
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Expand Up @@ -50,7 +50,7 @@ If executing from BigSky cluster:

```bash
# Step 4.) spack load snakemake and depdenencies
source /gs1/RTS/OpenOmics/bin/dependencies.sh
source /data/openomics/bin/dependencies.sh
```

### Execution
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30 changes: 15 additions & 15 deletions scripts/config.py
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Expand Up @@ -206,20 +206,20 @@ def get_tmp_dir(host):
"cynomac": "/vf/users/OpenOmics/references/genomes/cynomac/v2/GCF_012559485.2_MFA1912RKSv2_genomic.fna.gz",
},
"bigsky": {
"hg19": "/gs1/RTS/OpenOmics/references/genomes/human/hg19/GRCh37.primary_assembly.genome.fa.gz",
"grch37": "/gs1/RTS/OpenOmics/references/genomes/human/GRCh37/GRCh37.primary_assembly.genome.fa.gz",
"hg38": "/gs1/RTS/OpenOmics/references/genomes/human/hg38/GRCh38.p14.genome.fa.gz",
"grch38": "/gs1/RTS/OpenOmics/references/genomes/human/GRCh38/GRCh38.p14.genome.fa.gz",
"mm9": "/gs1/RTS/OpenOmics/references/genomes/mouse/mm9/mm9.fa.gz",
"grcm37": "/gs1/RTS/OpenOmics/references/genomes/mouse/GRCm37/mm9.fa.gz",
"mm10": "/gs1/RTS/OpenOmics/references/genomes/mouse/mm10/GRCm38.p4.genome.fa.gz",
"grcm38": "/gs1/RTS/OpenOmics/references/genomes/mouse/GRCm38/GRCm38.p4.genome.fa.gz",
"mm39": "/gs1/RTS/OpenOmics/references/genomes/mouse/mm39/GRCm39.genome.fa.gz",
"grcm39": "/gs1/RTS/OpenOmics/references/genomes/mouse/GRCm39/GRCm39.genome.fa.gz",
"rhemac10": "/gs1/RTS/OpenOmics/references/genomes/rhesus/rhe10/rheMac10.fa.gz",
"mmul10": "/gs1/RTS/OpenOmics/references/genomes/rhesus/mmul10/rheMac10.fa.gz",
"agm": "/gs1/RTS/OpenOmics/references/genomes/agm/1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz",
"mesaur": "/gs1/RTS/OpenOmics/references/genomes/mesaur/2.0/GCF_017639785.1_BCM_Maur_2.0_genomic.fna.gz",
"cynomac": "/gs1/RTS/OpenOmics/references/genomes/cynomac/v2/GCF_012559485.2_MFA1912RKSv2_genomic.fna.gz",
"hg19": "/data/openomics/references/genomes/human/hg19/GRCh37.primary_assembly.genome.fa.gz",
"grch37": "/data/openomics/references/genomes/human/GRCh37/GRCh37.primary_assembly.genome.fa.gz",
"hg38": "/data/openomics/references/genomes/human/hg38/GRCh38.p14.genome.fa.gz",
"grch38": "/data/openomics/references/genomes/human/GRCh38/GRCh38.p14.genome.fa.gz",
"mm9": "/data/openomics/references/genomes/mouse/mm9/mm9.fa.gz",
"grcm37": "/data/openomics/references/genomes/mouse/GRCm37/mm9.fa.gz",
"mm10": "/data/openomics/references/genomes/mouse/mm10/GRCm38.p4.genome.fa.gz",
"grcm38": "/data/openomics/references/genomes/mouse/GRCm38/GRCm38.p4.genome.fa.gz",
"mm39": "/data/openomics/references/genomes/mouse/mm39/GRCm39.genome.fa.gz",
"grcm39": "/data/openomics/references/genomes/mouse/GRCm39/GRCm39.genome.fa.gz",
"rhemac10": "/data/openomics/references/genomes/rhesus/rhe10/rheMac10.fa.gz",
"mmul10": "/data/openomics/references/genomes/rhesus/mmul10/rheMac10.fa.gz",
"agm": "/data/openomics/references/genomes/agm/1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz",
"mesaur": "/data/openomics/references/genomes/mesaur/2.0/GCF_017639785.1_BCM_Maur_2.0_genomic.fna.gz",
"cynomac": "/data/openomics/references/genomes/cynomac/v2/GCF_012559485.2_MFA1912RKSv2_genomic.fna.gz",
},
}