Adding sylph version 0.6.0 (#961)

* adding sylph version 0.6.0

* adjusted tests

README.md

@@ -274,7 +274,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [SRA-toolkit](https://hub.docker.com/r/staphb/sratoolkit/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sratoolkit)](https://hub.docker.com/r/staphb/sratoolkit) | <ul><li>2.9.2</li><li>[3.0.7](./sratoolkit/3.0.7/)</li></ul> | https://github.com/ncbi/sra-tools |
 | [SRST2](https://hub.docker.com/r/staphb/srst2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/srst2)](https://hub.docker.com/r/staphb/srst2) | <ul><li>0.2.0</li><li>[0.2.0 + custom Vibrio cholerae database](srst2/0.2.0-vibrio-230224/README.md)</li></ul> | https://github.com/katholt/srst2 |
 | [Staramr](https://hub.docker.com/r/staphb/staramr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/staramr)](https://hub.docker.com/r/staphb/staramr) | <ul><li>[0.5.1](./staramr/0.5.1/)</li><li>[0.7.1](./staramr/0.7.1/)</li><li>[0.8.0](./staramr/0.8.0/)</li><li>[0.10.0](./staramr/0.10.0/)</li></ul> | https://github.com/phac-nml/staramr |
-| [sylph](https://hub.docker.com/r/staphb/sylph) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sylph)](https://hub.docker.com/r/staphb/sylph) | <ul><li>[0.4.1](./sylph/0.4.1)</li><li>[0.5.1](./sylph/0.5.1)</li></ul> | https://github.com/bluenote-1577/sylph |
+| [sylph](https://hub.docker.com/r/staphb/sylph) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sylph)](https://hub.docker.com/r/staphb/sylph) | <ul><li>[0.4.1](./sylph/0.4.1)</li><li>[0.5.1](./sylph/0.5.1)</li><li>[0.6.0](./sylph/0.6.0)</li></ul> | https://github.com/bluenote-1577/sylph |
 | [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | <ul><li>[4.3.0](./tbprofiler/4.3.0/)</li><li>[4.4.0](./tbprofiler/4.4.0/)</li><li>[4.4.2](./tbprofiler/4.4.2/)</li><li>[5.0.1](tbprofiler/5.0.1/)</li></ul> | https://github.com/jodyphelan/TBProfiler |
 | [TipToft](https://hub.docker.com/r/staphb/tiptoft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | <ul><li>1.0.0</li><li>1.0.2</li></ul> | https://github.com/andrewjpage/tiptoft |
 | [Tostadas](https://hub.docker.com/r/staphb/tostadas/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) | <ul><li>[0.2.0-beta](./tostadas/0.2.0-beta/)</li><li>[3.1.0](./tostadas/3.1.0/)</li></ul> | https://github.com/CDCgov/tostadas |

sylph/0.6.0/Dockerfile

@@ -0,0 +1,63 @@
+ARG SYLPH_VER="0.6.0"
+
+## Builder ##
+FROM rust:1.74 as builder
+
+ARG SYLPH_VER
+
+RUN apt update && \
+    apt install -y cmake && \
+    wget -q https://github.com/bluenote-1577/sylph/archive/refs/tags/v${SYLPH_VER}.tar.gz && \
+    tar -xvf v${SYLPH_VER}.tar.gz && \
+    cd sylph-${SYLPH_VER} && \
+    cargo install --path . --root ~/.cargo && \
+    chmod +x /root/.cargo/bin/sylph
+
+## App ##
+FROM ubuntu:jammy as app
+
+ARG SYLPH_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="sylph"
+LABEL software.version=${SYLPH_VER}
+LABEL description="sylph is a program that can perform ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples."
+LABEL website="https://github.com/bluenote-1577/sylph"
+LABEL license="https://github.com/bluenote-1577/sylph/blob/main/LICENSE"
+LABEL maintainer="Stephen Turner"
+LABEL maintainer.email="[email protected]"
+
+# copy app from builder stage
+COPY --from=builder /root/.cargo/bin/sylph /usr/local/bin/sylph
+
+# default run command
+CMD sylph -h
+
+# singularity compatibility
+ENV LC_ALL=C
+
+# final working directory in app layer is /data
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+# making sure sylph is in PATH
+RUN sylph -h
+
+ARG SYLPH_VER
+
+RUN apt update && apt install -y wget
+
+WORKDIR /test
+
+COPY --from=builder /sylph-${SYLPH_VER}/test_files/* /test
+
+RUN date && \
+    sylph sketch -i e.coli-*.fasta.gz -o database && \
+    sylph sketch o157_reads.fastq.gz  && \
+    sylph query database.syldb *.sylsp > ani_queries.tsv && \
+    sylph profile database.syldb *.sylsp > profiling.tsv && \
+    cat *.tsv && \
+    date

sylph/0.6.0/README.md

@@ -0,0 +1,28 @@
+# sylph container
+
+Main tool : [sylph](https://github.com/bluenote-1577/sylph)
+
+Full documentation: https://github.com/bluenote-1577/sylph/wiki
+
+sylph is a program that can perform ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples.
+
+## Example Usage
+
+```bash
+# all fasta -> one *.syldb; fasta are assumed to be genomes
+sylph sketch genome1.fa genome2.fa -o database
+#EQUIVALENT: sylph sketch -g genome1.fa genome2.fa -o database
+
+# multi-sample sketching of paired reads
+sylph sketch -1 A_1.fq B_1.fq -2 A_2.fq B_2.fq -d output_read_sketch_folder
+
+# multi-sample sketching for single end reads, fastq are assumed to be reads
+sylph sketch reads.fq 
+#EQUIVALENT: sylph sketch -r reads.fq
+
+# ANI querying 
+sylph query database.syldb *.sylsp -t (threads) > ani_queries.tsv
+
+# taxonomic profiling 
+sylph profile database.syldb *.sylsp -t (threads) > profiling.tsv
+```