From 31e5d760101aa9d047b40151f81f7d86c79de5ed Mon Sep 17 00:00:00 2001
From: edu <eduardperezmendez@gmail.com>
Date: Wed, 9 Oct 2024 12:34:41 +0200
Subject: [PATCH 1/3] Created pod5 dockerfile

---
 pod5/DOCKERFILE | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 pod5/DOCKERFILE

diff --git a/pod5/DOCKERFILE b/pod5/DOCKERFILE
new file mode 100644
index 00000000..cf5d0df5
--- /dev/null
+++ b/pod5/DOCKERFILE
@@ -0,0 +1,30 @@
+################## BASE IMAGE ######################
+
+FROM biocontainers/biocontainers:v1.0.0_cv4
+
+################## METADATA ######################
+
+ARG software_version=0.3.15
+LABEL base_image="biocontainers:v1.0.0_cv4"
+LABEL version="1"
+LABEL software="pod5"
+LABEL software.version="$software_version"
+LABEL about.summary="The pod5 python module can be used to read and write nanopore reads stored in POD5 files"
+LABEL about.home="https://github.com/nanoporetech/pod5-file-format"
+LABEL about.documentation="https://pod5-file-format.readthedocs.io/en/latest/index.html"
+LABEL about.license_file="https://github.com/nanoporetech/pod5-file-format"
+LABEL about.license_file="https://github.com/nanoporetech/pod5-file-format/blob/master/LICENSE.md"
+LABEL about.license="Mozilla Public License 2.0"
+LABEL about.tags="Genomics"
+LABEL extra.identifiers.biotools="POD5"
+LABEL extra.binaries="pod5"
+
+################## MAINTAINER ######################
+LABEL maintainer="Eduard Perez Mendez <mail@eperezme.com>"
+
+
+################## INSTALLATION ####################
+RUN pip install pod5==$software_version
+
+WORKDIR /data/
+

From 90dacf822b709a601f1dec35a365ef3baf29bf4e Mon Sep 17 00:00:00 2001
From: edu <eduardperezmendez@gmail.com>
Date: Wed, 9 Oct 2024 13:32:08 +0200
Subject: [PATCH 2/3] Created Dockerfile for pod5

---
 pod5/DOCKERFILE | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/pod5/DOCKERFILE b/pod5/DOCKERFILE
index cf5d0df5..f032e467 100644
--- a/pod5/DOCKERFILE
+++ b/pod5/DOCKERFILE
@@ -1,18 +1,17 @@
 ################## BASE IMAGE ######################
 
-FROM biocontainers/biocontainers:v1.0.0_cv4
+FROM python:3.11-slim
 
 ################## METADATA ######################
 
 ARG software_version=0.3.15
-LABEL base_image="biocontainers:v1.0.0_cv4"
+LABEL base_image="python:3.11-slim"
 LABEL version="1"
 LABEL software="pod5"
 LABEL software.version="$software_version"
 LABEL about.summary="The pod5 python module can be used to read and write nanopore reads stored in POD5 files"
 LABEL about.home="https://github.com/nanoporetech/pod5-file-format"
 LABEL about.documentation="https://pod5-file-format.readthedocs.io/en/latest/index.html"
-LABEL about.license_file="https://github.com/nanoporetech/pod5-file-format"
 LABEL about.license_file="https://github.com/nanoporetech/pod5-file-format/blob/master/LICENSE.md"
 LABEL about.license="Mozilla Public License 2.0"
 LABEL about.tags="Genomics"
@@ -22,9 +21,14 @@ LABEL extra.binaries="pod5"
 ################## MAINTAINER ######################
 LABEL maintainer="Eduard Perez Mendez <mail@eperezme.com>"
 
-
 ################## INSTALLATION ####################
-RUN pip install pod5==$software_version
 
-WORKDIR /data/
+WORKDIR /app
+
+RUN apt-get update \
+    && pip install --upgrade pip \
+    && pip install lib-pod5==0.3.15 pod5==$software_version \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
 
+################## ENTRYPOINT ######################
+ENTRYPOINT ["/bin/bash"]

From 40081e8ae76c606bdb88823c29db54143cf53644 Mon Sep 17 00:00:00 2001
From: edu <eduardperezmendez@gmail.com>
Date: Wed, 9 Oct 2024 14:44:50 +0200
Subject: [PATCH 3/3] Updated to work with nextflow pipelines

---
 pod5/{DOCKERFILE => Dockerfile} | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)
 rename pod5/{DOCKERFILE => Dockerfile} (89%)

diff --git a/pod5/DOCKERFILE b/pod5/Dockerfile
similarity index 89%
rename from pod5/DOCKERFILE
rename to pod5/Dockerfile
index f032e467..311a395e 100644
--- a/pod5/DOCKERFILE
+++ b/pod5/Dockerfile
@@ -15,7 +15,7 @@ LABEL about.documentation="https://pod5-file-format.readthedocs.io/en/latest/ind
 LABEL about.license_file="https://github.com/nanoporetech/pod5-file-format/blob/master/LICENSE.md"
 LABEL about.license="Mozilla Public License 2.0"
 LABEL about.tags="Genomics"
-LABEL extra.identifiers.biotools="POD5"
+LABEL extra.identifiers.biotools="pod5"
 LABEL extra.binaries="pod5"
 
 ################## MAINTAINER ######################
@@ -25,10 +25,11 @@ LABEL maintainer="Eduard Perez Mendez <mail@eperezme.com>"
 
 WORKDIR /app
 
-RUN apt-get update \
+RUN apt-get update && apt-get install -y --no-install-recommends bash \
+    procps \
     && pip install --upgrade pip \
     && pip install lib-pod5==0.3.15 pod5==$software_version \
     && apt-get clean && rm -rf /var/lib/apt/lists/*
 
 ################## ENTRYPOINT ######################
-ENTRYPOINT ["/bin/bash"]
+CMD ["bash"]