Updating remaining /gs1 bigsky paths

Author: skchronicles

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 <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
@@ -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
@@ -114,4 +114,4 @@ Same sbatch execution as bigsky/skyline.
 
 ```bash
 sbatch weave_script.sbatch
-```
+```

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="<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:
@@ -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.

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

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",
     },
 }