#395 paths fix

antigenomics · Nov 12, 2024 · 0e5964c · 0e5964c
1 parent 729e9d2
commit 0e5964c
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/Dockerfile_2 b/Dockerfile_2
@@ -87,8 +87,8 @@ RUN mkdir -p /software/bin/
 RUN unzip vdjtools-1.2.1.zip
 RUN cp -r vdjtools-1.2.1/* /software/bin/
 RUN chmod +x /software/bin/vdjtools
-RUN cd /software/bin/
-RUN git clone https://github.com/antigenomics/mirpy.git
+#RUN cd /software/bin/
+#RUN git clone https://github.com/antigenomics/mirpy.git
 
 ENV PATH="/usr/lib/jvm/java-8-openjdk-amd64/bin:${PATH}"
 ENV PATH="/software/bin:${PATH}"

diff --git a/docker.sh b/docker.sh
@@ -4,6 +4,7 @@ cd vcs
 echo $(pwd)
 git clone https://github.com/antigenomics/vdjdb-db vdjdb-db
 git clone https://github.com/antigenomics/vdjdb-motifs vdjdb-motifs
+git clone https://github.com/antigenomics/mirpy.git
 cd vdjdb-db
 git checkout pyVDJdb
 echo $(pwd)

diff --git a/py_src/DefaultDBGenerator.py b/py_src/DefaultDBGenerator.py
@@ -4,15 +4,15 @@
 from ChunkQC import SIGNATURE_COLS, METHOD_COLUMNS, META_COLUMNS
 import sys
 
-sys.path.append('/software/bin/')
-sys.path.append('/software/bin/mirpy')
+sys.path.append('../../')
+sys.path.append('../../mirpy')
 
 from mirpy.mir.basic import pgen
 
-olga_pgen_human_trb = pgen.OlgaModel(model='../mirpy/mir/resources/olga/default_models/human_T_beta')
-olga_pgen_human_tra = pgen.OlgaModel(model='../mirpy/mir/resources/olga/default_models/human_T_alpha')
-olga_pgen_mouse_trb = pgen.OlgaModel(model='../mirpy/mir/resources/olga/default_models/mouse_T_beta')
-olga_pgen_mouse_tra = pgen.OlgaModel(model='../mirpy/mir/resources/olga/default_models/mouse_T_alpha')
+olga_pgen_human_trb = pgen.OlgaModel(model='../../mirpy/mir/resources/olga/default_models/human_T_beta')
+olga_pgen_human_tra = pgen.OlgaModel(model='../../mirpy/mir/resources/olga/default_models/human_T_alpha')
+olga_pgen_mouse_trb = pgen.OlgaModel(model='../../mirpy/mir/resources/olga/default_models/mouse_T_beta')
+olga_pgen_mouse_tra = pgen.OlgaModel(model='../../mirpy/mir/resources/olga/default_models/mouse_T_alpha')
 
 
 models_dict = {