| ... | ... |
@@ -85,12 +85,12 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
|
| 85 | 85 |
} |
| 86 | 86 |
|
| 87 | 87 |
for(assay in SummarizedExperiment::assayNames(newSce)) {
|
| 88 |
- if(!base::inherits(SummarizedExperiment::assay(sce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
|
|
| 89 |
- SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay)) |
|
| 88 |
+ if(!base::inherits(SummarizedExperiment::assay(newSce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
|
|
| 89 |
+ SummarizedExperiment::assay(newSce, assay) <- .convertToMatrix(SummarizedExperiment::assay(newSce, assay)) |
|
| 90 | 90 |
} |
| 91 | 91 |
|
| 92 |
- if(!base::inherits(SummarizedExperiment::assay(sce, assay), "DelayedArray") && isTRUE(delayedArray)) {
|
|
| 93 |
- SummarizedExperiment::assay(sce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(sce, assay)) |
|
| 92 |
+ if(!base::inherits(SummarizedExperiment::assay(newSce, assay), "DelayedArray") && isTRUE(delayedArray)) {
|
|
| 93 |
+ SummarizedExperiment::assay(newSce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(newSce, assay)) |
|
| 94 | 94 |
} |
| 95 | 95 |
} |
| 96 | 96 |
|
| ... | ... |
@@ -313,7 +313,7 @@ The usage of each argument is the same as running command line analysis. Here is |
| 313 | 313 |
|
| 314 | 314 |
``` |
| 315 | 315 |
docker run --rm -v /path/to/data:/SCTK_docker \ |
| 316 |
--it campbio/sctk_qc:1.7.5 \ |
|
| 316 |
+-it campbio/sctk_qc:1.7.6 \ |
|
| 317 | 317 |
-b /SCTK_docker/cellranger \ |
| 318 | 318 |
-P CellRangerV3 \ |
| 319 | 319 |
-s pbmc_100x100 \ |
| ... | ... |
@@ -328,7 +328,7 @@ docker run --rm -v /path/to/data:/SCTK_docker \ |
| 328 | 328 |
The Singulatiry image can easily be built using Docker Hub as a source: |
| 329 | 329 |
|
| 330 | 330 |
``` |
| 331 |
-singularity pull docker://campbio/sctk_qc:1.7.5 |
|
| 331 |
+singularity pull docker://campbio/sctk_qc:1.7.6 |
|
| 332 | 332 |
``` |
| 333 | 333 |
|
| 334 | 334 |
The usage of singleCellTK Singularity image is very similar to that of Docker. In Singularity 3.0+, the mount volume is [automatically overlaid](https://singularity.lbl.gov/docs-mount). |
| ... | ... |
@@ -337,7 +337,7 @@ It's recommended to re-set the home directory when you run singularity. Singular |
| 337 | 337 |
|
| 338 | 338 |
``` |
| 339 | 339 |
singularity run --home=/PathToSanitizedHome \ |
| 340 |
+--bind /PathToData:/data sctk_qc_1.7.6.sif \ |
|
| 340 | 341 |
-P CellRangerV3 \ |
| 341 | 342 |
-s gencodev34_pbmc_1k_v3 \ |
| 342 | 343 |
-b /data/gencodev34_pbmc_1k_v3 |
| ... | ... |
@@ -358,7 +358,7 @@ Also, you might want to specify cpu architecture when run the Singularity image |
| 358 | 358 |
#$ -pe omp 16 |
| 359 | 359 |
#$ -l cpu_arch=broadwell|haswell|skylake|cascadelake |
| 360 | 360 |
singularity run --home=/PathToSanitizedHome \ |
| 361 |
+--bind /PathToData:/data sctk_qc_1.7.6.sif \ |
|
| 361 | 362 |
-P CellRangerV3 \ |
| 362 | 363 |
-s gencodev34_pbmc_1k_v3 \ |
| 363 | 364 |
-b /data/gencodev34_pbmc_1k_v3 |
