From 68c037d885016bfde65eeae45acda4c18f6a6f9e Mon Sep 17 00:00:00 2001
From: nkleinbo <nils.kleinboelting@gmail.com>
Date: Wed, 23 Mar 2022 15:06:46 +0000
Subject: [PATCH 1/3] feat(docker): Custom image for prokka with support for
 partial genes added.

---
 docker/toolkit-prokka/Dockerfile | 54 ++++++++++++++++++++++++++++++++
 docker/toolkit-prokka/VERSION    |  1 +
 2 files changed, 55 insertions(+)
 create mode 100644 docker/toolkit-prokka/Dockerfile
 create mode 100644 docker/toolkit-prokka/VERSION

diff --git a/docker/toolkit-prokka/Dockerfile b/docker/toolkit-prokka/Dockerfile
new file mode 100644
index 00000000..97e19e0d
--- /dev/null
+++ b/docker/toolkit-prokka/Dockerfile
@@ -0,0 +1,54 @@
+FROM ubuntu:18.04
+
+# metadata
+LABEL website="https://github.com/tseemann/prokka"
+LABEL license="https://github.com/tseemann/prokka#licence"
+
+# install dependencies
+RUN apt-get update && \
+    apt-get -y install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl hmmer wget \
+                       zlib1g-dev python liblzma-dev libbz2-dev xz-utils curl g++ make &&\ 
+    apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+#get Bioperl
+#RUN cpan Bio::Perl
+
+# install bedtools 2.29.0 since >=2.27.0 is required for barrnap and the apt-get package is 2.25.0
+# dependencies required for bedtools: zlib1g-dev python liblzma-dev libbz2-dev xz-utils curl g++
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz && \
+  tar -zxf bedtools-2.29.0.tar.gz && \
+  rm bedtools-2.29.0.tar.gz && \
+  cd bedtools2 && \
+  make
+
+# add bedtools to PATH for barrnap test
+ENV PATH="$PATH:/bedtools2/bin"
+
+# install barrnap
+RUN wget https://github.com/tseemann/barrnap/archive/0.9.tar.gz &&\
+    tar -zxf 0.9.tar.gz &&\
+    rm 0.9.tar.gz &&\
+    cd barrnap-0.9 &&\
+    make test
+
+#get prokka
+RUN git clone https://github.com/tseemann/prokka && \
+    cd prokka && \
+    git fetch origin pull/219/head:partialgenes && \
+    git checkout partialgenes
+
+# install tbl2asn manually since the one included with prokka is expired.
+RUN wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O linux64.tbl2asn.gz && \
+    gunzip linux64.tbl2asn.gz && \
+    mv linux64.tbl2asn /usr/bin/tbl2asn && \
+    chmod 755 /usr/bin/tbl2asn
+
+# put prokka in PATH & 
+# set PATH to prioritize /usr/bin/tbl2asn before /prokka/binaries/tbl2asn
+ENV PATH="$PATH:/prokka/bin"
+
+#setupdb
+RUN prokka --setupdb
+
+WORKDIR /data
+
diff --git a/docker/toolkit-prokka/VERSION b/docker/toolkit-prokka/VERSION
new file mode 100644
index 00000000..6e8bf73a
--- /dev/null
+++ b/docker/toolkit-prokka/VERSION
@@ -0,0 +1 @@
+0.1.0

From e0d16bffd9c7fc55e157ffd17d730277ca63632c Mon Sep 17 00:00:00 2001
From: nkleinbo <nils.kleinboelting@gmail.com>
Date: Thu, 24 Mar 2022 11:21:46 +0000
Subject: [PATCH 2/3] feat(docker): small changes to reduce the size of the
 prokka image.

---
 docker/toolkit-prokka/Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docker/toolkit-prokka/Dockerfile b/docker/toolkit-prokka/Dockerfile
index 97e19e0d..3be76406 100644
--- a/docker/toolkit-prokka/Dockerfile
+++ b/docker/toolkit-prokka/Dockerfile
@@ -6,8 +6,9 @@ LABEL license="https://github.com/tseemann/prokka#licence"
 
 # install dependencies
 RUN apt-get update && \
-    apt-get -y install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl hmmer wget \
-                       zlib1g-dev python liblzma-dev libbz2-dev xz-utils curl g++ make &&\ 
+    apt-get -y --no-install-recommends install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl hmmer wget \
+                       zlib1g-dev python liblzma-dev libbz2-dev xz-utils curl g++ make \
+                       less bzip2 gzip libidn11-dev &&\ 
     apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*
 
 #get Bioperl

From dd71c2299f6fbb62b3cf1670623d9a5faa4db736 Mon Sep 17 00:00:00 2001
From: nkleinbo <nils.kleinboelting@gmail.com>
Date: Tue, 29 Mar 2022 14:24:53 +0000
Subject: [PATCH 3/3] feat(docker): Changed version format

---
 docker/toolkit-prokka/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/toolkit-prokka/VERSION b/docker/toolkit-prokka/VERSION
index 6e8bf73a..069f0f28 100644
--- a/docker/toolkit-prokka/VERSION
+++ b/docker/toolkit-prokka/VERSION
@@ -1 +1 @@
-0.1.0
+1.12.0-0