diff --git a/config/bigsky.json b/config/bigsky.json
index 9266e2b..fabb577 100644
--- a/config/bigsky.json
+++ b/config/bigsky.json
@@ -1,5 +1,5 @@
{
- "sif": "/gs1/RTS/OpenOmics/SIFs/",
+ "sif": "/data/openomics/SIFs/",
"mounts": {
"kaiju": {
"to": "/opt/kaiju",
diff --git a/docs/execution.md b/docs/execution.md
index c335ca4..02569f6 100644
--- a/docs/execution.md
+++ b/docs/execution.md
@@ -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
- **Bigsky: `/gs1/RTS/OpenOmics/bin/dependencies.sh`**
+ Dependency files for skyline and bigsky are now the same
+ **Bigsky: `/data/openomics/bin/dependencies.sh`**
**Skyline: `/data/openomics/bin/dependencies.sh`**
```bash
@@ -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
- **Bigsky: `/gs1/RTS/OpenOmics/bin/dependencies.sh`**
+ Dependency files for skyline and bigsky are now the same
+ **Bigsky: `/data/openomics/bin/dependencies.sh`**
**Skyline: `/data/openomics/bin/dependencies.sh`**
```bash
@@ -114,4 +114,4 @@ Same sbatch execution as bigsky/skyline.
```bash
sbatch weave_script.sbatch
-```
\ No newline at end of file
+```
diff --git a/docs/install.md b/docs/install.md
index 4f31b88..c56df9b 100644
--- a/docs/install.md
+++ b/docs/install.md
@@ -37,7 +37,7 @@ Biowulf uses environmental modules to control software. After executing the abov
> [+] Loading singularity 4.X.X on cnXXXX
```bash title="Bigsky"
-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:
@@ -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.
diff --git a/docs/usage/run.md b/docs/usage/run.md
index 114e76a..5aa2aef 100644
--- a/docs/usage/run.md
+++ b/docs/usage/run.md
@@ -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
diff --git a/scripts/config.py b/scripts/config.py
index 288b9f2..cc4565b 100644
--- a/scripts/config.py
+++ b/scripts/config.py
@@ -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",
},
}
\ No newline at end of file