Merge 583c85b into 48754c0

CHANGELOG.md

@@ -25,6 +25,7 @@ pdfmerger: v1.0
 picardtools: 2.23.4 -> 2.25.0
 sambamba: 0.6.8-h682856c_0 -> 0.8.0-h984e79f_0
 samtools: 1.10-h9402c20_2 -> 1.11-h6270b1f_0
+smncopynumbercaller: 4b2c1ad -> v1.1.1
 stranger: 0.7 -> 0.7.1
 tiddit: 2.8.1 -> 2.12.1
 

containers/smncopynumbercaller/Dockerfile

@@ -5,9 +5,9 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="2"
+LABEL version="3"
 LABEL software="SMNCopyNumberCaller"
-LABEL software.version="1.0"
+LABEL software.version="v1.1.1"
 LABEL extra.binaries="smn_caller"
 LABEL maintainer="Clinical-Genomics/MIP"
 
@@ -17,17 +17,17 @@ RUN conda install pip python=3.7 numpy scipy pysam statsmodels
 RUN /opt/conda/bin/conda clean -tipsy
 
 ## Download
-RUN wget --no-verbose https://github.com/Illumina/SMNCopyNumberCaller/archive/v1.0.zip -O /opt/conda/share/smncopynumbercaller-v.1.0.zip
+RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/SMNCopyNumberCaller/archive/v1.1.1.zip -O /opt/conda/share/smncopynumbercaller-v.1.1.1.zip
 
 ## Extract
-RUN unzip -o /opt/conda/share/smncopynumbercaller-v.1.0.zip -d /opt/conda/share/
+RUN unzip -o /opt/conda/share/smncopynumbercaller-v.1.1.1.zip -d /opt/conda/share/
 
 ## Move to smn_caller directory
-RUN cd /opt/conda/share/SMNCopyNumberCaller-1.0 && \
+RUN cd /opt/conda/share/SMNCopyNumberCaller-1.1.1 && \
     chmod a+x smn_caller.py
 
-RUN ln --symbolic --force /opt/conda/share/SMNCopyNumberCaller-1.0/smn_caller.py /opt/conda/bin/smn_caller.py
+RUN ln --symbolic --force /opt/conda/share/SMNCopyNumberCaller-1.1.1/smn_caller.py /opt/conda/bin/smn_caller.py
 
-RUN ln --symbolic --force /opt/conda/share/SMNCopyNumberCaller-1.0/data /opt/conda/bin/data
+RUN ln --symbolic --force /opt/conda/share/SMNCopyNumberCaller-1.1.1/data /opt/conda/bin/data
 
 WORKDIR /data/

documentation/Setup.md

@@ -59,7 +59,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [rtg-tools] (version: 3.10.1)
 - [Sambamba] (version: 0.8.0)
 - [Samtools] (version: 1.11)
-- [SMNCopyNumberCaller] (version: 4b2c1ad)
+- [SMNCopyNumberCaller] (version: v1.1.1)
 - [Stranger] (version: 0.7)
 - [Svdb] (version: 2.2.0)
 - [Telomerecat] (version: 3.4.0)

t/data/test_data/miptest_install_config.yaml

@@ -174,7 +174,7 @@ container:
   smncopynumbercaller:
     executable:
       smn_caller.py:
-    uri: docker.io/clinicalgenomics/smncopynumbercaller:4b2c1ad
+    uri: docker.io/clinicalgenomics/smncopynumbercaller:v1.1.1
   star:
     executable:
       STAR:

templates/mip_install_config.yaml

@@ -177,7 +177,7 @@ container:
   smncopynumbercaller:
     executable:
       smn_caller.py:
-    uri: docker.io/clinicalgenomics/smncopynumbercaller:4b2c1ad
+    uri: docker.io/clinicalgenomics/smncopynumbercaller:v1.1.1
   star:
     executable:
       STAR:

templates/program_test_cmds.yaml

@@ -82,6 +82,8 @@ sambamba:
   execution: 'sambamba --version'
 samtools:
   execution: 'samtools --version'
+smncopynumbercaller:
+  execution: 'smn_caller.py'
 star:
   execution: 'STAR'
 star-fusion: