Docker image creation for bpwrapper

Author: rocky

.travis.yml

@@ -12,9 +12,8 @@ after_failure:
 
 install:
   # Prerequisites
-  # libdb-dev (Berkeley DB headers) seems to be needed by BioPerl
   # By running cpanm this way without testing rather than using ./Build,
-  # we save *a lot* of time
+  # we save *a lot* of time.
   - "cpanm --notest --force $PREREQS"
 
 script:

Dockerfile

@@ -0,0 +1,17 @@
+FROM ubuntu:bionic
+
+LABEL name bpwrapper
+LABEL src "https://github.com/bioperl/p5-bpwrapper"
+LABEL creator rocky
+LABEL desc "command-line utilites for Bio::Perl"
+
+RUN apt update \
+  && apt upgrade -y \
+  && apt install -y git perl cpanminus make gcc libexpat1-dev
+
+RUN cpanm --notest Module::Build rlib XML::Parser XML::DOM::XPath Test::More Bio::Restriction::Analysis
+
+RUN git clone --depth=10 https://github.com/bioperl/p5-bpwrapper.git p5-bpwrapper \
+ && cd p5-bpwrapper && perl ./Build.PL && ./Build && make install
+ENV PATH="/usr/local/bin:${PATH}"
+CMD /bin/bash

GNUmakefile

@@ -6,6 +6,7 @@ BASH ?= bash
 all: Build
 	$(PERL) Build --makefile_env_macros 1
 
+#: make Build program
 Build:
 	$(PERL) Build.PL || $(PERL) Makefile.PL
 
@@ -20,6 +21,10 @@ clean: Build
         lib/Bio/BPWrapper*.check \
 	lib/Bio/BPWrapper/*.check || /bin/true
 
+#: Create a docker image
+docker:
+	docker build -t rockyb/bpwrapper .
+
 code: Build
 	$(PERL) Build --makefile_env_macros 1 code
 

README.md

@@ -58,6 +58,35 @@ The git code generally has the newest code. If git is not your thing, you can al
 
 ```
 
+# Install and run from docker
+
+Use the bpwrapper docker image. It includes `bioaln`, `biodb`, `biopop`, `bioseq`, and `biotree`.
+
+To download the image so that docker recognizes it:
+
+```console
+docker pull rockyb/bpwrapper
+```
+
+For things other than getting help, you'll often need to pass a data in file to the program. Do that by sharing the
+directory that the file is in on the `docker` invocation.
+
+You'll need to pay attention to the permissions on the data file its
+directory. The docker container runs as as a user that may not have
+access to data. I've found however that if you put the data in `/tmp`
+files will be seen inside the running docker container.
+
+For example:
+
+```console
+$ cp test-data/cds.fas /tmp/cds.fas
+$ docker run -it -v /tmp:/test-files rockyb/bpwrapper bioseq -l /test-files/cds.fas
+DK2	120
+W70332	120
+M1608	108
+F2
+```
+
 # Developers, Contact, Citation
 * Yözen Hernández
 * Pedro Pagan