From 522f561cfe5331679f384b8960e0df33c227f879 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Wed, 15 Nov 2023 20:28:21 +0000
Subject: [PATCH 1/2] adding version 1.11.1

---
 README.md                |  2 +-
 medaka/1.11.1/Dockerfile | 70 ++++++++++++++++++++++++++++++++++++++++
 medaka/1.11.1/README.md  | 26 +++++++++++++++
 3 files changed, 97 insertions(+), 1 deletion(-)
 create mode 100644 medaka/1.11.1/Dockerfile
 create mode 100644 medaka/1.11.1/README.md

diff --git a/README.md b/README.md
index 5288daccf..863e0bd75 100644
--- a/README.md
+++ b/README.md
@@ -176,7 +176,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Mash](https://hub.docker.com/r/staphb/mash/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mash)](https://hub.docker.com/r/staphb/mash)  | <ul><li>2.1</li><li>2.2</li><li>2.3</li></ul> | https://github.com/marbl/Mash |
 | [mashtree](https://hub.docker.com/r/staphb/mashtree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mashtree)](https://hub.docker.com/r/staphb/mashtree) | <ul><li>0.52.0</li><li>0.57.0</li><li>1.0.4</li><li>1.2.0</li></ul> | https://github.com/lskatz/mashtree |
 | [MaSuRCA](https://hub.docker.com/r/staphb/masurca) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/masurca)](https://hub.docker.com/r/staphb/masurca) | <ul><li>4.0.8</li><li>4.0.9</li><li>4.1.0</li></ul> | https://github.com/alekseyzimin/masurca |
-| [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>0.8.1</li><li>1.0.1</li><li>1.2.0</li></ul> | https://github.com/nanoporetech/medaka |
+| [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>0.8.1</li><li>1.0.1</li><li>1.2.0</li><li>1.2.0</li><li>[1.11.1](./medaka/1.11.1/)</li></ul> | https://github.com/nanoporetech/medaka |
 | [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <ul><li>3.0.3-no-db (no database)</li><li> 3.0.3 (~3GB db) | https://github.com/biobakery/MetaPhlAn/tree/3.0 |
 | [MIDAS](https://hub.docker.com/r/staphb/midas) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) | <ul><li>1.3.2 (no database)</li> | https://github.com/snayfach/MIDAS |
 | [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li></ul> | https://github.com/lh3/minimap2 |
diff --git a/medaka/1.11.1/Dockerfile b/medaka/1.11.1/Dockerfile
new file mode 100644
index 000000000..ba102c4ad
--- /dev/null
+++ b/medaka/1.11.1/Dockerfile
@@ -0,0 +1,70 @@
+FROM mambaorg/micromamba:1.5.1 as app
+
+ARG MEDAKA_VER=1.11.1
+ARG PYABPOA_VER=1.2.4
+
+LABEL base.image="mambaorg/micromamba:1.5.1"
+LABEL dockerfile.version="1"
+LABEL software="medaka"
+LABEL software.version="${MEDAKA_VER}"
+LABEL description="For polishing assemblies with nanopore reads"
+LABEL website="https://github.com/nanoporetech/medaka"
+LABEL license="https://github.com/nanoporetech/medaka/blob/master/LICENSE.md"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+USER root
+WORKDIR /
+
+# install dependencies (most are for pyabpoa)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    gcc \
+    make \
+    pkg-config \
+    zlib1g-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    libssl-dev && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# setting PATH
+ENV PATH="${PATH}:/opt/conda/bin/" \
+    LC_ALL=C.UTF-8
+
+# no version here because the medaka on conda lags behind the latest release
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults medaka && \
+    micromamba clean -a -y && \
+    mkdir /data
+
+# this _should_ overwrite the medaka installed via micromamba
+RUN /opt/conda/bin/pip install medaka==${MEDAKA_VER} && \
+    /opt/conda/bin/pip install pyabpoa==${PYABPOA_VER} && \
+    medaka --version
+
+CMD medaka --help
+
+WORKDIR /data
+
+# A second FROM insruction creates a new stage
+# new base for testing
+FROM app as test
+
+# print help and version info; check dependencies (not all software has these options available)
+# Mostly this ensures the tool of choice is in path and is executable
+RUN medaka --help && \
+    medaka --version
+    
+# set working directory so that all test inputs & outputs are kept in /test
+WORKDIR /test
+
+# using on real data (CRPA isolate)
+RUN wget -q https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_021601745.3 -O GCA_021601745.3.fasta && \
+    wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR234/068/SRR23473168/SRR23473168_1.fastq.gz && \
+    medaka_consensus -i SRR23473168_1.fastq.gz -d GCA_021601745.3.fasta -o testing -t 4
+
+# listing available models
+RUN medaka tools list\_models
diff --git a/medaka/1.11.1/README.md b/medaka/1.11.1/README.md
new file mode 100644
index 000000000..e81e0584d
--- /dev/null
+++ b/medaka/1.11.1/README.md
@@ -0,0 +1,26 @@
+# medaka container
+
+Main tool : [medaka](https://github.com/nanoporetech/medaka)
+
+Full documentation: [https://github.com/nanoporetech/medaka](https://github.com/nanoporetech/medaka)
+
+> medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. It provides state-of-the-art results outperforming sequence-graph based methods and signal-based methods, whilst also being faster.
+
+## Example Usage
+
+```bash
+
+# listing models
+medaka tools list\_models
+
+# polishing
+medaka_consensus -i sample.fastq.gz -d sample.fasta -o medaka/sample -t 4
+
+```
+
+## Medaka models
+
+Medaka updates frequently. These are the medaka models in this image:
+```
+Available: r103_fast_g507, r103_fast_snp_g507, r103_fast_variant_g507, r103_hac_g507, r103_hac_snp_g507, r103_hac_variant_g507, r103_min_high_g345, r103_min_high_g360, r103_prom_high_g360, r103_prom_snp_g3210, r103_prom_variant_g3210, r103_sup_g507, r103_sup_snp_g507, r103_sup_variant_g507, r1041_e82_260bps_fast_g632, r1041_e82_260bps_fast_variant_g632, r1041_e82_260bps_hac_g632, r1041_e82_260bps_hac_v4.0.0, r1041_e82_260bps_hac_v4.1.0, r1041_e82_260bps_hac_variant_g632, r1041_e82_260bps_hac_variant_v4.1.0, r1041_e82_260bps_sup_g632, r1041_e82_260bps_sup_v4.0.0, r1041_e82_260bps_sup_v4.1.0, r1041_e82_260bps_sup_variant_g632, r1041_e82_260bps_sup_variant_v4.1.0, r1041_e82_400bps_fast_g615, r1041_e82_400bps_fast_g632, r1041_e82_400bps_fast_variant_g615, r1041_e82_400bps_fast_variant_g632, r1041_e82_400bps_hac_g615, r1041_e82_400bps_hac_g632, r1041_e82_400bps_hac_v4.0.0, r1041_e82_400bps_hac_v4.1.0, r1041_e82_400bps_hac_v4.2.0, r1041_e82_400bps_hac_variant_g615, r1041_e82_400bps_hac_variant_g632, r1041_e82_400bps_hac_variant_v4.1.0, r1041_e82_400bps_hac_variant_v4.2.0, r1041_e82_400bps_sup_g615, r1041_e82_400bps_sup_v4.0.0, r1041_e82_400bps_sup_v4.1.0, r1041_e82_400bps_sup_v4.2.0, r1041_e82_400bps_sup_variant_g615, r1041_e82_400bps_sup_variant_v4.1.0, r1041_e82_400bps_sup_variant_v4.2.0, r104_e81_fast_g5015, r104_e81_fast_variant_g5015, r104_e81_hac_g5015, r104_e81_hac_variant_g5015, r104_e81_sup_g5015, r104_e81_sup_g610, r104_e81_sup_variant_g610, r10_min_high_g303, r10_min_high_g340, r941_e81_fast_g514, r941_e81_fast_variant_g514, r941_e81_hac_g514, r941_e81_hac_variant_g514, r941_e81_sup_g514, r941_e81_sup_variant_g514, r941_min_fast_g303, r941_min_fast_g507, r941_min_fast_snp_g507, r941_min_fast_variant_g507, r941_min_hac_g507, r941_min_hac_snp_g507, r941_min_hac_variant_g507, r941_min_high_g303, r941_min_high_g330, r941_min_high_g340_rle, r941_min_high_g344, r941_min_high_g351, r941_min_high_g360, r941_min_sup_g507, r941_min_sup_snp_g507, r941_min_sup_variant_g507, r941_prom_fast_g303, r941_prom_fast_g507, r941_prom_fast_snp_g507, r941_prom_fast_variant_g507, r941_prom_hac_g507, r941_prom_hac_snp_g507, r941_prom_hac_variant_g507, r941_prom_high_g303, r941_prom_high_g330, r941_prom_high_g344, r941_prom_high_g360, r941_prom_high_g4011, r941_prom_snp_g303, r941_prom_snp_g322, r941_prom_snp_g360, r941_prom_sup_g507, r941_prom_sup_snp_g507, r941_prom_sup_variant_g507, r941_prom_variant_g303, r941_prom_variant_g322, r941_prom_variant_g360, r941_sup_plant_g610, r941_sup_plant_variant_g610
+```

From 5bf294ad4de24abb9a651fce40dd00d9576d32b4 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Fri, 1 Dec 2023 18:57:55 +0000
Subject: [PATCH 2/2] updated 1.11.1 to 1.11.2

---
 README.md                            | 2 +-
 medaka/{1.11.1 => 1.11.2}/Dockerfile | 4 ++--
 medaka/{1.11.1 => 1.11.2}/README.md  | 0
 3 files changed, 3 insertions(+), 3 deletions(-)
 rename medaka/{1.11.1 => 1.11.2}/Dockerfile (97%)
 rename medaka/{1.11.1 => 1.11.2}/README.md (100%)

diff --git a/README.md b/README.md
index 863e0bd75..ea399df68 100644
--- a/README.md
+++ b/README.md
@@ -176,7 +176,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Mash](https://hub.docker.com/r/staphb/mash/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mash)](https://hub.docker.com/r/staphb/mash)  | <ul><li>2.1</li><li>2.2</li><li>2.3</li></ul> | https://github.com/marbl/Mash |
 | [mashtree](https://hub.docker.com/r/staphb/mashtree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mashtree)](https://hub.docker.com/r/staphb/mashtree) | <ul><li>0.52.0</li><li>0.57.0</li><li>1.0.4</li><li>1.2.0</li></ul> | https://github.com/lskatz/mashtree |
 | [MaSuRCA](https://hub.docker.com/r/staphb/masurca) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/masurca)](https://hub.docker.com/r/staphb/masurca) | <ul><li>4.0.8</li><li>4.0.9</li><li>4.1.0</li></ul> | https://github.com/alekseyzimin/masurca |
-| [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>0.8.1</li><li>1.0.1</li><li>1.2.0</li><li>1.2.0</li><li>[1.11.1](./medaka/1.11.1/)</li></ul> | https://github.com/nanoporetech/medaka |
+| [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>[0.8.1](./medaka/0.8.1)</li><li>[1.0.1](./medaka/1.0.1/)</li><li>[1.2.0](./medaka/1.2.0/)</li><li>[1.2.0](./medaka/1.2.0/)</li><li>[1.11.2](./medaka/1.11.2/)</li></ul> | https://github.com/nanoporetech/medaka |
 | [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <ul><li>3.0.3-no-db (no database)</li><li> 3.0.3 (~3GB db) | https://github.com/biobakery/MetaPhlAn/tree/3.0 |
 | [MIDAS](https://hub.docker.com/r/staphb/midas) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) | <ul><li>1.3.2 (no database)</li> | https://github.com/snayfach/MIDAS |
 | [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li></ul> | https://github.com/lh3/minimap2 |
diff --git a/medaka/1.11.1/Dockerfile b/medaka/1.11.2/Dockerfile
similarity index 97%
rename from medaka/1.11.1/Dockerfile
rename to medaka/1.11.2/Dockerfile
index ba102c4ad..9cb8a9b9e 100644
--- a/medaka/1.11.1/Dockerfile
+++ b/medaka/1.11.2/Dockerfile
@@ -1,6 +1,6 @@
 FROM mambaorg/micromamba:1.5.1 as app
 
-ARG MEDAKA_VER=1.11.1
+ARG MEDAKA_VER=1.11.2
 ARG PYABPOA_VER=1.2.4
 
 LABEL base.image="mambaorg/micromamba:1.5.1"
@@ -67,4 +67,4 @@ RUN wget -q https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_021601745.3 -O GCA_0
     medaka_consensus -i SRR23473168_1.fastq.gz -d GCA_021601745.3.fasta -o testing -t 4
 
 # listing available models
-RUN medaka tools list\_models
+RUN medaka tools list\_models
\ No newline at end of file
diff --git a/medaka/1.11.1/README.md b/medaka/1.11.2/README.md
similarity index 100%
rename from medaka/1.11.1/README.md
rename to medaka/1.11.2/README.md