fix: update main project path based on repo name change and reorg.

angelettilab · Aug 6, 2020 · ece6a8e · ece6a8e
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commit ece6a8e
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Showing 20 changed files with 22 additions and 22 deletions.
diff --git a/reports/RNA_analysis.Rmd b/reports/RNA_analysis.Rmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(echo = F, results = 'hide', fig.width=10)
 
 ```{r}
 # specify relevant directory information
-pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/'  # parent directiory
+pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/'  # parent directiory
 adir <- paste0(pdir,'analysis/')  # analysis subdirectory
 ddir <- paste0(pdir,'data/')  # data subdirectory
 ```

diff --git a/reports/trajectory_analysis.Rmd b/reports/trajectory_analysis.Rmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(echo = F, results = 'hide', fig.width=10)
 
 ```{r}
 # specify relevant directory information
-pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/'  # parent directiory
+pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/'  # parent directiory
 adir <- paste0(pdir,'analysis/')  # analysis subdirectory
 ddir <- paste0(pdir,'data/')  # data subdirectory
 cdir <- paste0(adir,'06_cluster/')  # clustering subdirectory

diff --git a/scripts/RNA_velocity/rna_velocity_analysis.R b/scripts/RNA_velocity/rna_velocity_analysis.R
@@ -1,6 +1,6 @@
 
 # specify relevant directories
-projdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
+projdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu'
 loomdir <- paste0(projdir, '/data/rna_velocity/loom_files')
 velodir <- paste0(projdir, '/analysis/rna_velocity')
 if (!dir.exists(velodir)) { dir.create(velodir, recursive=T) }
@@ -74,7 +74,7 @@ emat <- merged_data$spliced
 nmat <- merged_data$unspliced
 
 # load Seurat object
-DATA <- readRDS('/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/analysis/04_cluster/seurat_object.rds')
+DATA <- readRDS('/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/analysis/04_cluster/seurat_object.rds')
 
 # subset Seurat object to only include cells in loom files
 DATA <- subset(DATA, cells=colnames(DATA)[colnames(DATA) %in% colnames(emat)])

diff --git a/scripts/RNA_velocity/run_velo.sh b/scripts/RNA_velocity/run_velo.sh
@@ -7,6 +7,6 @@
 #SBATCH --mail-type=END
 #SBATCH -o run_velo.log
 
-singularity run ~/projects/d_angeletti_1910/envs/rna_velocity/velocyto.sif bash ~/projects/d_angeletti_1910/scripts/velocyto_get_spliced_unspliced.sh
+singularity run ~/projects/d_angeletti_1910/scMouseBcellFlu/envs/rna_velocity/velocyto.sif bash ~/projects/d_angeletti_1910/scMouseBcellFlu/scripts/velocyto_get_spliced_unspliced.sh
 
 
diff --git a/scripts/RNA_velocity/velocyto_get_spliced_unspliced.sh b/scripts/RNA_velocity/velocyto_get_spliced_unspliced.sh
@@ -3,7 +3,7 @@
 ########################
 ### DEFINE VARIABLES ###
 ########################
-main='/home/jonrob/projects/d_angeletti_1910'
+main='/home/jonrob/projects/d_angeletti_1910/scMouseBcellFlu'
 data_path='/crex/proj/snic2019-8-255/private/jay/filezila/2019/10x_cellranger_26_apr'
 annot_path=$main/'data/rna_velocity/genome_annotation_files'
 

diff --git a/scripts/VDJ_analysis/VDJ_lineage_reconstruction.R b/scripts/VDJ_analysis/VDJ_lineage_reconstruction.R
@@ -7,7 +7,7 @@ library(dplyr)
 
 
 # specify directory containing genotyped VDJ files
-proj_dir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/'
+proj_dir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/'
 geno_dir <- paste0(proj_dir, 'analysis/immcantation/genotyping/')
 
 # get list of available files

diff --git a/scripts/VDJ_analysis/immcantation_VDJ_workflow.sh b/scripts/VDJ_analysis/immcantation_VDJ_workflow.sh
@@ -6,7 +6,7 @@
 ### DEFINE DIRECTORIES ###
 ##########################
 # specify main project directory
-main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
+main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu'
 
 
 ###########################

diff --git a/scripts/plotting/gen_RNA_analysis_plots.R b/scripts/plotting/gen_RNA_analysis_plots.R
@@ -10,7 +10,7 @@ suppressMessages(suppressWarnings({
 }))
 
 # specify relevant directories
-pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/'  # project directiory
+pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/'  # project directiory
 adir <- paste0(pdir,'analysis/')  # analysis subdirectory
 ddir <- paste0(pdir,'data/')  # data subdirectory
 

diff --git a/scripts/plotting/gen_trajectory_slingshot_plots.R b/scripts/plotting/gen_trajectory_slingshot_plots.R
@@ -11,7 +11,7 @@ suppressMessages(suppressWarnings({
 }))
 
 # specify relevant directories
-pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/'  # project directiory
+pdir <- '/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/'  # project directiory
 adir <- paste0(pdir,'analysis/')  # analysis subdirectory
 
 

diff --git a/scripts/plotting/umap3d.R b/scripts/plotting/umap3d.R
@@ -11,7 +11,7 @@ gg_color_hue <- function(n) {
 }
 
 # load Seurat object
-DATA <- readRDS('/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/analysis/06_cluster/seurat_object.rds')
+DATA <- readRDS('/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/analysis/06_cluster/seurat_object.rds')
 
 # run UMAP
 DATA <- RunUMAP(object = DATA, assay="RNA", reduction="mnn", dims=1:50, n.components=3, n.neighbors=50, spread=5,
@@ -31,5 +31,5 @@ p_State <- plot_ly(df, x=~umap3_1, y=~umap3_2, z=~umap3_3,color=~cluster_use,
                    colors=pal, alpha=1, alpha_stroke=0, size=0.1) %>%  add_markers() %>%
   layout(scene = list(xaxis = list(title = 'UMAP_1'), yaxis = list(title = 'UMAP_2'),zaxis = list(title = 'UMAP_3')))
 ggplotly(p_State, height=800, width=800)
-saveWidget(p_State, "/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/analysis/06_cluster/umap_plots/3d_umap.html")
+saveWidget(p_State, "/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu/analysis/06_cluster/umap_plots/3d_umap.html")
 
diff --git a/scripts/scRNAseq_pipeline/run_wf.sh b/scripts/scRNAseq_pipeline/run_wf.sh
@@ -7,6 +7,6 @@
 #SBATCH --mail-type=END
 #SBATCH -o run_wf.log
 
-singularity run ~/projects/d_angeletti_1910/scripts/sauron/sauron.sif bash ~/projects/d_angeletti_1910/scripts/scRNAseq_pipeline/run_workflow.sh
+singularity run ~/projects/d_angeletti_1910/scMouseBcellFlu/scripts/sauron/sauron.sif bash ~/projects/d_angeletti_1910/scMouseBcellFlu/scripts/scRNAseq_pipeline/run_workflow.sh
 
 
diff --git a/scripts/scRNAseq_pipeline/run_workflow.sh b/scripts/scRNAseq_pipeline/run_workflow.sh
@@ -5,7 +5,7 @@
 ########################
 var_to_plot='dataset,mouse_nr,day_post_infection,organ,infection'
 var_to_regress='nCount_RNA,nFeature_RNA,perc_mito,CC.Diff'  # regress CC.Diff (S - G2M) instead of S and G2M separately
-main='/home/jonrob/projects/d_angeletti_1910'
+main='/home/jonrob/projects/d_angeletti_1910/scMouseBcellFlu'
 script_path='/home/jonrob/repos/sauron/scripts'
 
 cd $main

diff --git a/scripts/scanpy/convert_seurat_to_anndata.sh b/scripts/scanpy/convert_seurat_to_anndata.sh
@@ -4,7 +4,7 @@
 # AnnData object (.h5ad file) in the same directory
 
 # Specify paths
-main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
+main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910/scMouseBcellFlu'
 seurat_object=$main'/analysis/06_cluster/seurat_object.rds'
 
 cd $main

diff --git a/scripts/test/workflow_mito.sh b/scripts/test/workflow_mito.sh
@@ -7,7 +7,7 @@ var_to_plot='dataset,mouse_nr,day_post_infection,organ,infection'
 var_to_regress='nCount_RNA,nFeature_RNA,perc_mito,CC.Diff'  # regress CC.Diff (S - G2M) instead of S and G2M separately
 # main='/home/jonrob/projects/d_angeletti_1910'
 # script_path='/home/jonrob/repos/sauron/scripts'
-main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910'
+main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910/scMouseBcellFlu'
 script_path='/cephyr/users/jonrob/Hebbe/repos/sauron/scripts'
 # main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
 # script_path='/Users/jonrob/Documents/NBIS/repos/sauron/scripts'

diff --git a/scripts/test/workflow_no_integration.sh b/scripts/test/workflow_no_integration.sh
@@ -7,7 +7,7 @@ var_to_plot='dataset,mouse_nr,day_post_infection,organ,infection'
 var_to_regress='nFeature_RNA,percent_mito,S.Score,G2M.Score'
 # main='/home/jonrob/projects/d_angeletti_1910'
 # script_path='/home/jonrob/repos/sauron/scripts'
-main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910'
+main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910/scMouseBcellFlu'
 script_path='/cephyr/users/jonrob/Hebbe/repos/sauron/scripts'
 # main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
 # script_path='/Users/jonrob/Documents/NBIS/repos/sauron/scripts'

diff --git a/scripts/test/workflow_no_scale.sh b/scripts/test/workflow_no_scale.sh
@@ -9,7 +9,7 @@
 ########################
 var_to_plot='dataset,mouse_nr,day_post_infection,organ,infection'
 var_to_regress='nFeature_RNA,percent_mito,S.Score,G2M.Score'
-main='/home/jonrob/projects/d_angeletti_1910'
+main='/home/jonrob/projects/d_angeletti_1910/scMouseBcellFlu'
 script_path='/home/jonrob/repos/sauron/scripts'
 # main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
 # script_path='/Users/jonrob/Documents/NBIS/repos/sauron/scripts'

diff --git a/scripts/test/workflow_scaleCC_integrate.sh b/scripts/test/workflow_scaleCC_integrate.sh
@@ -7,7 +7,7 @@ var_to_plot='dataset,mouse_nr,day_post_infection,organ,infection'
 var_to_regress='nCount_RNA,nFeature_RNA,perc_mito,S.Score,G2M.Score'
 # main='/home/jonrob/projects/d_angeletti_1910'
 # script_path='/home/jonrob/repos/sauron/scripts'
-main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910'
+main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910/scMouseBcellFlu'
 script_path='/cephyr/users/jonrob/Hebbe/repos/sauron/scripts'
 # main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
 # script_path='/Users/jonrob/Documents/NBIS/repos/sauron/scripts'

diff --git a/scripts/test/workflow_scale_integrate.sh b/scripts/test/workflow_scale_integrate.sh
@@ -7,7 +7,7 @@ var_to_plot='dataset,mouse_nr,day_post_infection,organ,infection'
 var_to_regress='nCount_RNA,nFeature_RNA,perc_mito,CC.Diff'  # regress CC.Diff (S - G2M) instead of S and G2M separately
 # main='/home/jonrob/projects/d_angeletti_1910'
 # script_path='/home/jonrob/repos/sauron/scripts'
-main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910'
+main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910/scMouseBcellFlu'
 script_path='/cephyr/users/jonrob/Hebbe/repos/sauron/scripts'
 # main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'
 # script_path='/Users/jonrob/Documents/NBIS/repos/sauron/scripts'

diff --git a/scripts/trajectory/run_tr.sh b/scripts/trajectory/run_tr.sh
@@ -7,6 +7,6 @@
 #SBATCH --mail-type=END
 #SBATCH -o run_tr.log
 
-singularity run ~/projects/d_angeletti_1910/envs/trajectory/trajectory.sif bash ~/projects/d_angeletti_1910/scripts/run_trajectory.sh
+singularity run ~/projects/d_angeletti_1910/scMouseBcellFlu/envs/trajectory/trajectory.sif bash ~/projects/d_angeletti_1910/scMouseBcellFlu/scripts/run_trajectory.sh
 
 
diff --git a/scripts/trajectory/run_trajectory_slingshot.sh b/scripts/trajectory/run_trajectory_slingshot.sh
@@ -3,7 +3,7 @@
 ########################
 ### DEFINE VARIABLES ###
 ########################
-main='/home/jonrob/projects/d_angeletti_1910'
+main='/home/jonrob/projects/d_angeletti_1910/scMouseBcellFlu'
 # main='/cephyr/users/jonrob/Hebbe/projects/d_angeletti_1910'
 # main='/Users/jonrob/Documents/NBIS/LTS_projects/d_angeletti_1910'