Merge pull request #806 from Kincekara/ispcr

adds isPcr

Program_Licenses.md

@@ -58,6 +58,7 @@ The licenses of the open-source software that is contained in these Docker image
 | iqtree | GNU GPLv2 | https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE |
 | iqtree2 | GNU GPLv2 | https://github.com/iqtree/iqtree2/blob/master/LICENSE |
 | IRMA | GNU GPLv3 | https://wonder.cdc.gov/amd/flu/irma/disclaimer.html |
+| isPcr | non-standard - see README in source | https://hgwdev.gi.ucsc.edu/~kent/src/isPcr33.zip |
 | iVar | GNU GPLv3 | https://github.com/andersen-lab/ivar/blob/master/LICENSE |
 | Kaptive |  GNU GPLv3 | https://github.com/katholt/Kaptive/blob/master/LICENSE |
 | Kleborate | GNU GPLv3 | https://github.com/katholt/Kleborate/blob/master/LICENSE |

README.md

@@ -162,6 +162,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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/ |
 | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | <ul><li>2.1.2</li><li>2.2.2.2</li><li>[2.2.2.6](iqtree2/2.2.2.6/)</li></ul> | http://www.iqtree.org/ |
 | [IRMA](https://hub.docker.com/r/staphb/irma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | <ul><li>1.0.2</li><li>1.0.3</li><li>1.1.2</li><li>1.1.3</li></ul> | https://wonder.cdc.gov/amd/flu/irma/|
+| [isPcr](https://users.soe.ucsc.edu/~kent/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ispcr)](https://hub.docker.com/r/staphb/ispcr) | <ul><li>[33](ispcr/33/)</li></ul> | https://users.soe.ucsc.edu/~kent/ |
 | [iVar](https://hub.docker.com/r/staphb/ivar/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | <ul><li>1.1</li><li>1.1 (+SARS-CoV2 reference)</li><li>1.2.1</li><li>1.2.1 (+SC2 ref)</li><li>1.2.2 (+SC2 ref and artic bedfiles)</li><li>1.3</li><li>1.3.1</li><li>1.3.2</li><li>1.4.1</li><li>1.4.2</li></ul> | https://github.com/andersen-lab/ivar |
 | [Kaptive](https://hub.docker.com/r/staphb/kaptive/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | <ul><li>2.0.0</li><li>2.0.3</li><li>2.0.5</li></ul> | https://github.com/katholt/Kaptive/ |
 | [Kleborate](https://hub.docker.com/r/staphb/kleborate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | <ul><li>2.0.4</li><li>2.1.0</li><li>2.2.0</li><li>2.3.2</li><li>[2.3.2-2023-05](kleborate/2.3.2-2023-05/README.md)</li></ul> | https://github.com/katholt/Kleborate/ <br/> https://github.com/katholt/Kaptive/ |

ispcr/33/Dockerfile

@@ -0,0 +1,57 @@
+ARG ISPCR_VER="33"
+
+## Builder ##
+FROM ubuntu:jammy as builder
+
+ARG ISPCR_VER
+ARG MACHTYPE="x86_64-pc-linux-gnu"
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    wget \
+    unzip
+
+RUN wget https://hgwdev.gi.ucsc.edu/~kent/src/isPcr${ISPCR_VER}.zip &&\
+    unzip isPcr${ISPCR_VER}.zip &&\
+    cd isPcrSrc &&\
+    sed -i 's/-Werror//g' inc/common.mk &&\
+    mkdir -p bin/$MACHTYPE &&\
+    mkdir -p lib/$MACHTYPE &&\
+    make HOME=$PWD MACHTYPE=${MACHTYPE} C_INCLUDE_PATH=/usr/include LIBRARY_PATH=/usr/lib CFLAGS="-fcommon" &&\
+    mv bin/$MACHTYPE/* /usr/local/bin/
+
+## App ##
+FROM ubuntu:jammy as app 
+
+ARG ISPCR_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="isPcr"
+LABEL software.version="${ISPCR_VER}"
+LABEL description="In-Slico PCR"
+LABEL website="https://users.soe.ucsc.edu/~kent/"
+LABEL license="All modules are copyright 2000-2004 by Jim Kent. License is hereby granted for personal, academic, and non-profit use."
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+
+ENV LC_ALL=C
+
+CMD [ "isPcr" ]
+
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+# prepare inputs
+RUN apt-get update && apt-get install -y wget &&\
+    wget https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/bigZips/wuhCor1.fa.gz &&\
+    gunzip wuhCor1.fa.gz &&\
+    echo "orf1a CTAGGACCTCTTTCTGCTCA ACACTCTCCTAGCACCATCA" > primers
+
+# run a test
+RUN isPcr wuhCor1.fa primers stdout
+

ispcr/33/README.md

@@ -0,0 +1,29 @@
+# isPcr container
+
+Main tool: [isPcr](https://users.soe.ucsc.edu/~kent/)
+
+Code repository: https://hgwdev.gi.ucsc.edu/~kent/src/
+
+Basic information on how to use this tool:
+- executable: isPcr
+- help:
+- version:
+- description: In-Slico PCR
+
+Additional information:
+
+```
+usage:
+   isPcr database query output   
+where database is a fasta, nib, or twoBit file or a text file containing
+a list of these files,  query is a text file file containing three columns: name,
+forward primer, and reverse primer,  and output is where the results go.
+The names 'stdin' and 'stdout' can be used as file names to make using the
+program in pipes easier.
+```
+
+## Example Usage
+
+```bash
+isPcr template.fa primers.txt output
+```