map new drive

mskcc · Oct 16, 2023 · faf1c86 · faf1c86
1 parent 259304d
commit faf1c86
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/find_completed_runs_dag.py b/find_completed_runs_dag.py
@@ -105,7 +105,7 @@
       run_name_only = completed_run[7:]  # ex: MICHELLE_0461_AHMJFJDSX2
       samplesheet = "SampleSheet_" + completed_run + ".csv"
 
-      orig_samplesheet_dir = Variable.get("original_samplesheet_dir", default_var="/skimcs/mohibullahlab/LIMS/LIMS_SampleSheets/")
+      orig_samplesheet_dir = Variable.get("original_samplesheet_dir", default_var="/rtssdc/mohibullahlab/LIMS/LIMS_SampleSheets/")
       orig_samplesheet = orig_samplesheet_dir + samplesheet
       dest_samplesheet_dir = Variable.get("destination_samplesheet_dir", default_var="/igo/work/igo/SampleSheetCopies/")
       dest_samplesheet = dest_samplesheet_dir + samplesheet

diff --git a/scripts/Prepare-HiSeq-Tracker.sh b/scripts/Prepare-HiSeq-Tracker.sh
@@ -2,7 +2,7 @@
 #Example: sh ./Prepare-HiSeq-Tracker.sh MOMO_0125
 
 RUN=$1
-SAMPLESHEET="/skimcs/mohibullahlab/LIMS/LIMS_SampleSheets/SampleShee*"$RUN"*.csv"
+SAMPLESHEET="/rtssdc/mohibullahlab/LIMS/LIMS_SampleSheets/SampleShee*"$RUN"*.csv"
 
 #parse sample sheet to parameters
 

diff --git a/scripts/cellranger_multi.py b/scripts/cellranger_multi.py
@@ -64,7 +64,7 @@ def find_fastq_file(sample_ID_list):
 
 CONFIG_AREA = "/igo/stats/Multi_config/"
 DRIVE_LOCATION = "/igo/work/igo/Cellranger_Multi_Config/"
-ORIGIN_DRIVE_LOCATION = "/skimcs/mohibullahlab/LIMS/LIMS_cellranger_multi/"
+ORIGIN_DRIVE_LOCATION = "/rtssdc/mohibullahlab/LIMS/LIMS_cellranger_multi/"
 BAMTOFASTQ = "/igo/work/nabors/tools/cellranger-7.0.0/lib/bin/bamtofastq"
 STATS_AREA = "/igo/stats/PIPELINE/"
 # endpoint for cellranger multi

diff --git a/scripts/cellranger_spatial.py b/scripts/cellranger_spatial.py
@@ -9,7 +9,7 @@
 
 
 ENDPOINT = "https://igolims.mskcc.org:8443/LimsRest/getConfig?igoId="
-original_tiff_images_directory = "/skimcs/mohibullahlab/IGO_Pipeline_Results/Single_Cell/10X_Genomics/TIFF_Images/"
+original_tiff_images_directory = "/rtssdc/mohibullahlab/IGO_Pipeline_Results/Single_Cell/10X_Genomics/TIFF_Images/"
 tiff_images_directory = "/igo/work/igo/TIFF_Images/"
 
 

diff --git a/scripts/deliver_pipeline.py b/scripts/deliver_pipeline.py
@@ -108,7 +108,7 @@ def deliver_pipeline_output(project, pi, recipe):
     # TCR seq only need deliver manifest, those files located under viale lab drive
     # example file: /pskis34/LIMS/TCRseqManifest/Project_13545_TCRseq_Manifest_Beta.csv
     elif recipe == "TCRSeq-IGO":
-        pipeline_path_prefix = "/skimcs/mohibullahlab/LIMS/TCRseqManifest/Project_" + project + "_TCRseq"
+        pipeline_path_prefix = "/rtssdc/mohibullahlab/LIMS/TCRseqManifest/Project_" + project + "_TCRseq"
         TCR_delivery_folder = delivery_folder + "/Manifest"
         if not os.path.exists(TCR_delivery_folder):
                 print("Creating pipeline delivery folder {}".format(TCR_delivery_folder))