Scgpt update

src/methods/scgpt_finetuned/config.vsh.yaml

@@ -49,15 +49,7 @@ resources:
 engines:
   - type: docker
     image: openproblems/base_pytorch_nvidia:1
-    # TODO: Try to find working installation of flash attention (flash-attn<1.0.5)
     setup:
-      #- type: python
-      #  pypi:
-      #    - gdown
-      #    - scgpt # Install from PyPI to get dependencies
-      #- type: docker
-      #  # Force re-installing from GitHub to get bug fixes
-      #  run: pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
       - type: docker
         run: |
           git clone https://github.com/bowang-lab/scGPT && \

src/methods/scgpt_zeroshot/config.vsh.yaml

@@ -51,15 +51,6 @@ resources:
 engines:
   - type: docker
     image: openproblems/base_pytorch_nvidia:1
-    # TODO: Try to find working installation of flash attention (flash-attn<1.0.5)
-    setup:
-      #- type: python
-      #  pypi:
-      #    - gdown
-      #    - scgpt # Install from PyPI to get dependencies
-      #- type: docker
-      #  # Force re-installing from GitHub to get bug fixes
-      #  run: pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
       - type: docker
         run: |
           git clone https://github.com/bowang-lab/scGPT && \

src/methods/scprint/config.vsh.yaml

@@ -61,7 +61,7 @@ arguments:
   - name: --max_len
     type: integer
     description: The maximum length of the gene sequence.
-    default: 4000
+    default: 2300
 
 resources:
   - type: python_script
@@ -86,7 +86,7 @@ engines:
         script: from scdataloader.utils import populate_my_ontology; populate_my_ontology()
 runners:
   - type: executable
-   # docker_run_args: --gpus all
+    # docker_run_args: --gpus all
   - type: nextflow
     directives:
       label: [hightime, highmem, midcpu, gpu, highsharedmem]