TRTools (Hope's version) (#145)

* TRTools (Hope's version)

* Update Dockerfile

* trying to install poetry

* debug

* Update Dockerfile

* Update Dockerfile

* activate not run

* matt version

* lint

* absolute workdir

* remove second build

---------

Co-authored-by: Matt Welland <mattwellie@gmail.com>

images.toml

@@ -42,6 +42,7 @@ strvctvre = 'v.1.10'
 subread = '2.0.6'
 talos = '5.1.3'  # release to build, image names should have specific releases. Can build by naming side-branch
 trtools = '5.0.2'
+trtools_hope_version = 'skip-if-monomorphic'  # specific branch name
 vep_105 = '105.0'
 vep_110 = 'release_110.1'
 verifybamid = '2.0.1'

images/exomiser/Dockerfile

@@ -10,7 +10,7 @@ RUN mkdir /exomiser && \
     unzip "${EXOMISER_ARCHIVE}" && \
     rm "${EXOMISER_ARCHIVE}" && \
     echo '#!/bin/bash' >> /usr/local/bin/exomiser && \
-    echo cd /exomiser/${EXOMISER_STEM} \&\& exec java -jar $(echo /exomiser/${EXOMISER_STEM}/${EXOMISER_STEM}.jar) \"\$@\" >> /usr/local/bin/exomiser && \
+    echo cd /exomiser/${EXOMISER_STEM} \&\& exec java -jar /exomiser/${EXOMISER_STEM}/${EXOMISER_STEM}.jar \"\$@\" >> /usr/local/bin/exomiser && \
     chmod 755 /usr/local/bin/exomiser
 
 WORKDIR /exomiser/${EXOMISER_STEM}

images/trtools_hope_version/Dockerfile

@@ -0,0 +1,12 @@
+FROM python:3.10-bullseye
+
+ARG VERSION=${VERSION:-skip-if-monomorphic}
+ARG GIT_REPO=https://github.com/populationgenomics/TRTools.git
+
+# Install necessary packages and clean up to reduce image size
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    git curl bzip2 zip && \
+    rm -rf /var/lib/apt/lists/* && \
+    rm -rf /var/cache/apt/*
+
+RUN pip install --no-cache-dir metamist git+${GIT_REPO}@${VERSION}