From 528902c652fb8a8ecf3f5989be606fa268a69353 Mon Sep 17 00:00:00 2001 From: dhatribadri Date: Tue, 23 Apr 2024 12:05:52 -0400 Subject: [PATCH 1/7] Adding samclip 0.4.0 --- samclip/0.4.0/._Dockerfile | Bin 0 -> 4096 bytes samclip/0.4.0/._README.md | Bin 0 -> 4096 bytes samclip/0.4.0/Dockerfile | 55 +++++++++++++++++++++++++++++++++++++ samclip/0.4.0/README.md | 27 ++++++++++++++++++ 4 files changed, 82 insertions(+) create mode 100644 samclip/0.4.0/._Dockerfile create mode 100644 samclip/0.4.0/._README.md create mode 100644 samclip/0.4.0/Dockerfile create mode 100644 samclip/0.4.0/README.md diff --git a/samclip/0.4.0/._Dockerfile b/samclip/0.4.0/._Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..2e5f9315f6c112b86d9b7f6725de2b6c5506b1c6 GIT binary patch literal 4096 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDJkFz{^v(m+1nBL)UWIUpMX1Yitw+A$;~ z2q^XmqJv=pkd3aE5hw-~mrBmh)k`cW$Vt`9Nh~fYEly2INi0cK4hROSVW^s;mIk8j zUd&Yj(W78A1V%$(Gz3ONU^E0qLtr!nMnhmU1V%$(Gz3ONU^E19g#f6t3Bq6?7m|@# ztWcC%oL^d$oT`wPUzDwonOBmUSCW~Zmza}NsgRSJR-%xUlbDwc>$Vqox1Ojhs@R)|o50+1L3ClDJkFz{^v(m+1nBL)UWIUt(=a103v0xJ0e z)xiT~uSe6u0yGIEE(%1+`MG+D1qC^&dWEHlMTvPOnR%%|DMm#gA;7>Og^T(m4bHI{}l|aggfk72XF0~{Ps6Wvv+tKhyjd@P=i1bf(#UpIiu{+5Eu=C(GVC7fzc2c4S~@R7!85Z5Eu=C z(GVC70bmG#dQh-l6oXtyMrN@>QEG91X;E^jLRx-NwnAoJNh+}0nV*-KlT)dXlbTkd akd%{{mksO-4~GCm^*`K4G7NJ6{{sMkYi7s* literal 0 HcmV?d00001 diff --git a/samclip/0.4.0/Dockerfile b/samclip/0.4.0/Dockerfile new file mode 100644 index 000000000..a186e17bc --- /dev/null +++ b/samclip/0.4.0/Dockerfile @@ -0,0 +1,55 @@ +ARG SAMCLIP_VER="0.4.0" + +FROM ubuntu:jammy as app + +ARG SAMCLIP_VER + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="samclip" +LABEL software.version="${SAMCLIP_VER}" +LABEL description="Samclip: filter SAM file for soft and hard clipped alignments" +LABEL website="https://github.com/tseemann/samclip" +LABEL license="https://github.com/tseemann/samclip/blob/master/LICENSE" +LABEL maintainer="Dhatri Badri" +LABEL maintainer.email="dhatrib@umich.edu" + +# install dependencies +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + wget \ + software-properties-common \ + perl && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install samclip +RUN wget https://raw.githubusercontent.com/tseemann/samclip/master/samclip && \ + chmod +x samclip && \ + mkdir /data + +ENV PATH="${PATH}:/samclip-${SAMCLIP_VER}/" \ + LC_ALL=C + +CMD [ "./samclip", "--help" ] + +WORKDIR /data + +FROM app as test + +ARG SAMCLIP_VER + +# Copy the samclip executable from the app stage to the test stage +COPY --from=app /samclip /samclip + +RUN /samclip --help && \ + /samclip --version + +WORKDIR /test + +# Run test using samclip executable +RUN wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna && \ + wget https://raw.githubusercontent.com/tseemann/samclip/master/test.sam && \ + wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna.fai && \ + /samclip --ref test.fna < test.sam > out.sam + + \ No newline at end of file diff --git a/samclip/0.4.0/README.md b/samclip/0.4.0/README.md new file mode 100644 index 000000000..4d42a76d8 --- /dev/null +++ b/samclip/0.4.0/README.md @@ -0,0 +1,27 @@ +# Samclip container + +Main tool: [samclip](https://github.com/tseemann/samclip) + +Basic information on how to use this tool: +- executable: ./samclip +- help: -h, --help +- version: -V, --version +- description: Filter SAM file for soft and hard clipped alignments + +Additional tools: + +- [samtools](https://github.com/samtools/samtools) +- [bwa](https://github.com/lh3/bwa) + +## Example Usage + +Basic command to clip ends of reads +```bash +samclip --ref ref.fa < in.sam > out.sam +``` + +Integrate samclip with other tools like bwa and samtools +```bash +bwa mem ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam +``` + From c8ab1f87a40676e874e0822bee21fb71a7cebc18 Mon Sep 17 00:00:00 2001 From: dhatribadri Date: Tue, 23 Apr 2024 12:37:10 -0400 Subject: [PATCH 2/7] Adding samclip 0.4.0 --- samclip/0.4.0/._Dockerfile | Bin 4096 -> 4096 bytes samclip/0.4.0/Dockerfile | 2 -- 2 files changed, 2 deletions(-) diff --git a/samclip/0.4.0/._Dockerfile b/samclip/0.4.0/._Dockerfile index 2e5f9315f6c112b86d9b7f6725de2b6c5506b1c6..cd9e9c1e357b4626cff746501be1ba750fb1dd07 100644 GIT binary patch delta 31 lcmZorXi%82fT!)TdKv=|yzVMv+_=%0Z{h*g%}@Ab7y+}Y3mO0b delta 31 mcmZorXi%82fTwDXS{efo*u9vmv~i;`-^2r~o1gH>FaiLolnTE9 diff --git a/samclip/0.4.0/Dockerfile b/samclip/0.4.0/Dockerfile index a186e17bc..3a883aae7 100644 --- a/samclip/0.4.0/Dockerfile +++ b/samclip/0.4.0/Dockerfile @@ -51,5 +51,3 @@ RUN wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna && \ wget https://raw.githubusercontent.com/tseemann/samclip/master/test.sam && \ wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna.fai && \ /samclip --ref test.fna < test.sam > out.sam - - \ No newline at end of file From 688714f26c80a2d696d937717901633d65da04b0 Mon Sep 17 00:00:00 2001 From: dhatribadri Date: Wed, 1 May 2024 10:35:24 -0400 Subject: [PATCH 3/7] Removing hidden files --- samclip/0.4.0/._Dockerfile | Bin 4096 -> 0 bytes samclip/0.4.0/._README.md | Bin 4096 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 samclip/0.4.0/._Dockerfile delete mode 100644 samclip/0.4.0/._README.md diff --git a/samclip/0.4.0/._Dockerfile b/samclip/0.4.0/._Dockerfile deleted file mode 100644 index cd9e9c1e357b4626cff746501be1ba750fb1dd07..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4096 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDJkFz{^v(m+1nBL)UWIUpMX1Yitw+A$;~ z2q^XmqJv=pkd3aE5hw-~mrBmh)k`cW$Vt`9Nh~fYEly2INi0cK4hROSVQ71-o(7^{ zca?$kjDpb+7!85Z5Eu=C(GVC7fzc2c4S~@R7!85Z5Eu=C(Gb8H0-%l~yz?j*l95@g zP?TDnUs{x$s*sjnl&z4NSCX1nl9`{En3GefkdvBLqL7r6n3oOg3*$6&2uYy&AMS7& I2D$(L0b-3R;{X5v diff --git a/samclip/0.4.0/._README.md b/samclip/0.4.0/._README.md deleted file mode 100644 index 110294e07ceb59107550c3279141f5f276ceba37..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4096 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDJkFz{^v(m+1nBL)UWIUt(=a103v0xJ0e z)xiT~uSe6u0yGIEE(%1+`MG+D1qC^&dWEHlMTvPOnR%%|DMm#gA;7>Og^T(m4bHI{}l|aggfk72XF0~{Ps6Wvv+tKhyjd@P=i1bf(#UpIiu{+5Eu=C(GVC7fzc2c4S~@R7!85Z5Eu=C z(GVC70bmG#dQh-l6oXtyMrN@>QEG91X;E^jLRx-NwnAoJNh+}0nV*-KlT)dXlbTkd akd%{{mksO-4~GCm^*`K4G7NJ6{{sMkYi7s* From 19ad40e5799dd784aff10df9d51306fc1ee55064 Mon Sep 17 00:00:00 2001 From: dhatribadri Date: Wed, 1 May 2024 10:58:02 -0400 Subject: [PATCH 4/7] Adding samclip tool to the list of tools in program licenses --- Program_Licenses.md | 1 + 1 file changed, 1 insertion(+) diff --git a/Program_Licenses.md b/Program_Licenses.md index 5c335248f..afde8980f 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -141,6 +141,7 @@ The licenses of the open-source software that is contained in these Docker image | ResFinder | Apache 2.0 | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ | | Roary | GNU GPLv3 | https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE | | SalmID| MIT | https://github.com/hcdenbakker/SalmID/blob/master/LICENSE | +| samclip | GNU GPLv3 | https://github.com/tseemann/samclip/blob/master/LICENSE | | Samtools | GNU GPLv3 | https://github.com/samtools/samtools/blob/develop/LICENSE | | SeqKit | MIT | https://github.com/shenwei356/seqkit/blob/master/LICENSE | SeqSero | GNU GPLv2 | https://github.com/denglab/SeqSero/blob/master/LICENSE | From b115ffa2ed76d03bb631b7eae221322010665b4a Mon Sep 17 00:00:00 2001 From: dhatribadri Date: Wed, 1 May 2024 11:05:15 -0400 Subject: [PATCH 5/7] Adding samclip tool to the list of tools in README --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 2bf1fa88f..4ed6c9d56 100644 --- a/README.md +++ b/README.md @@ -247,6 +247,7 @@ To learn more about the docker pull rate limits and the open source software pro | [ResFinder](https://hub.docker.com/r/staphb/resfinder/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) |
  • [4.1.1](./resfinder/4.1.11/)
  • [4.5.0](./resfinder/4.5.0/)
| https://bitbucket.org/genomicepidemiology/resfinder/src/master/ | | [Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) |
  • 3.12.0
  • 3.13.0
| https://github.com/sanger-pathogens/Roary | | [SalmID](https://hub.docker.com/r/staphb/salmid)
[![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) |
  • 0.1.23
| https://github.com/hcdenbakker/SalmID | +| [samclip](https://hub.docker.com/r/staphb/samclip)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samclip)](https://hub.docker.com/r/staphb/samclip) |
  • [0.4.0](./samclip/0.4.0/)
| https://github.com/tseemann/samclip | | [Samtools](https://hub.docker.com/r/staphb/samtools)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) |
  • [1.9](./samtools/1.9/)
  • [1.10](./samtools/1.10/)
  • [1.11](./samtools/1.11/)
  • [1.12](./samtools/1.12/)
  • [1.13](./samtools/1.13/)
  • [1.14](./samtools/1.14/)
  • [1.15](./samtools/1.15/)
  • [1.16](./samtools/1.16/)
  • [1.16.1](./samtools/1.16.1/)
  • [1.17](./samtools/1.17/)
  • [1.17-2023-06](./samtools/1.17-2023-06/)
  • [1.18](./samtools/1.18/)
  • [1.19](./samtools/1.19/)
  • [1.20](./samtools/1.20/)
| https://github.com/samtools/samtools | | [SeqKit](https://hub.docker.com/r/staphb/SeqKit)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqkit)](https://hub.docker.com/r/staphb/seqkit) |
  • [2.3.1](./seqkit/2.3.1/)
  • [2.6.1](./seqkit/2.6.1/)
  • [2.7.0](./seqkit/2.7.0/)
  • [2.8.0](./seqkit/2.8.0/)
  • [2.8.1](./seqkit/2.8.1/)
| https://github.com/shenwei356/seqkit | | [SeqSero](https://hub.docker.com/r/staphb/seqsero/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero)](https://hub.docker.com/r/staphb/seqsero) |
  • 1.0.1
| https://github.com/denglab/SeqSero | From aeb804679ad5a96f4a8ed69fb4f8e627e5e43332 Mon Sep 17 00:00:00 2001 From: Dhatri Badri <56312676+dhatribadri@users.noreply.github.com> Date: Wed, 1 May 2024 14:17:33 -0400 Subject: [PATCH 6/7] Update Dockerfile based on Erin's feedback --- samclip/0.4.0/Dockerfile | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/samclip/0.4.0/Dockerfile b/samclip/0.4.0/Dockerfile index 3a883aae7..dd1fe7bb3 100644 --- a/samclip/0.4.0/Dockerfile +++ b/samclip/0.4.0/Dockerfile @@ -23,26 +23,23 @@ RUN apt-get update && \ apt-get autoclean && rm -rf /var/lib/apt/lists/* # install samclip -RUN wget https://raw.githubusercontent.com/tseemann/samclip/master/samclip && \ - chmod +x samclip && \ +RUN wget https://github.com/tseemann/samclip/archive/refs/tags/v${SAMCLIP_VER}.tar.gz && \ + tar -xvf v${SAMCLIP_VER}.tar.gz && \ + rm v${SAMCLIP_VER}.tar.gz && \ + chmod +x /samclip-${SAMCLIP_VER}/samclip && \ mkdir /data ENV PATH="${PATH}:/samclip-${SAMCLIP_VER}/" \ LC_ALL=C -CMD [ "./samclip", "--help" ] +CMD [ "samclip", "--help" ] WORKDIR /data FROM app as test -ARG SAMCLIP_VER - -# Copy the samclip executable from the app stage to the test stage -COPY --from=app /samclip /samclip - -RUN /samclip --help && \ - /samclip --version +RUN samclip --help && \ + samclip --version WORKDIR /test @@ -50,4 +47,4 @@ WORKDIR /test RUN wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna && \ wget https://raw.githubusercontent.com/tseemann/samclip/master/test.sam && \ wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna.fai && \ - /samclip --ref test.fna < test.sam > out.sam + samclip --ref test.fna < test.sam > out.sam From 752ef8559ee02c3bc4ab5b8d5ecda32c029fbde7 Mon Sep 17 00:00:00 2001 From: Dhatri Badri <56312676+dhatribadri@users.noreply.github.com> Date: Wed, 1 May 2024 14:18:31 -0400 Subject: [PATCH 7/7] Remove unnecessary lines of information from README.md --- samclip/0.4.0/README.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/samclip/0.4.0/README.md b/samclip/0.4.0/README.md index 4d42a76d8..ef19ee2f7 100644 --- a/samclip/0.4.0/README.md +++ b/samclip/0.4.0/README.md @@ -8,11 +8,6 @@ Basic information on how to use this tool: - version: -V, --version - description: Filter SAM file for soft and hard clipped alignments -Additional tools: - -- [samtools](https://github.com/samtools/samtools) -- [bwa](https://github.com/lh3/bwa) - ## Example Usage Basic command to clip ends of reads