Merge pull request #888 from Kincekara/hmmer

adds hmmer 3.4

README.md

@@ -164,7 +164,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [GenoVi](https://hub.docker.com/r/staphb/genovi) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genovi)](https://hub.docker.com/r/staphb/genovi) | <ul><li>[0.2.16](./genovi/0.2.16/)</li></ul> | https://github.com/robotoD/GenoVi |
 | [gfastats](https://hub.docker.com/r/staphb/gfastats) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gfastats)](https://hub.docker.com/r/staphb/gfastats) | <ul><li>1.3.6</li></ul> | https://github.com/vgl-hub/gfastats |
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <ul><li>[1.0.2c](./heatcluster/1.0.2c/)</li></ul> | https://github.com/DrB-S/heatcluster/tree/main |
-| [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li></ul> | http://hmmer.org/ |
+| [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |
 | [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li></ul> | https://www.htslib.org/ |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |

hmmer/3.4/Dockerfile

@@ -0,0 +1,53 @@
+ARG HMMER_VER="3.4"
+
+## Builder ##
+FROM ubuntu:jammy as builder
+
+ARG HMMER_VER
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    build-essential &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget http://eddylab.org/software/hmmer/hmmer-${HMMER_VER}.tar.gz &&\
+    tar -xvf hmmer-${HMMER_VER}.tar.gz &&\
+    cd hmmer-${HMMER_VER} &&\
+    ./configure &&\
+    make && make install
+
+## App ##
+FROM ubuntu:jammy as app
+
+ARG HMMER_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="HMMER"
+LABEL software.version="${HMMER_VER}"
+LABEL description="Biological sequence analysis using profile hidden Markov models"
+LABEL website="http://hmmer.org/"
+LABEL license="https://github.com/EddyRivasLab/hmmer/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+# get compiled binaries from builder
+COPY --from=builder /usr/local/bin/ /usr/local/bin/
+
+ENV LC_ALL=C
+
+CMD hmmbuild -h && hmmsearch -h
+
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+ARG HMMER_VER
+
+# get test data from source package 
+COPY --from=builder /hmmer-${HMMER_VER}/tutorial/* .
+
+RUN hmmbuild globins4.hmm globins4.sto &&\
+    hmmsearch globins4.hmm globins45.fa | tee test.out
+

hmmer/3.4/Readme.md

@@ -0,0 +1,44 @@
+# HMMER container
+
+Main tool : [HMMER](http://hmmer.org/)
+
+Code repository: https://github.com/EddyRivasLab/hmmer
+
+Basic information on how to use this tool:
+- executables:
+    - alimask
+    - hmmalign
+    - hmmbuild
+    - hmmconvert
+    - hmmemit
+    - hmmfetch
+    - hmmlogo
+    - hmmpgmd
+    - hmmpgmd_shard
+    - hmmpress
+    - hmmscan
+    - hmmsearch
+    - hmmsim
+    - hmmstat
+    - jackhmmer
+    - makehmmerdb
+    - nhmmer
+    - nhmmscan
+    - phmmer
+
+- help: -h
+- version: -v
+- description:
+>HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs).
+
+Full documentation: http://eddylab.org/software/hmmer/Userguide.pdf
+
+# Example commands 
+
+```bash
+# build a profile from an alignment
+hmmbuild hmm_file msa_file
+
+# search profile against a sequence database
+hmmsearch hmm_file seqs.fa
+```