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ncbi/rapt:v0.5.5

Manifest digest

sha256:8ff966b4c7e4d05b5f3f56489bd5aa97c3d83ccdfc61b66d02ce6f9b73b6fc38

OS/ARCH

linux/amd64

Compressed size

4.97 GB

Last pushed

over 1 year by gpipe

Type

Image

Manifest digest

sha256:8ff966b4c7e4d05b5f3f56489bd5aa97c3d83ccdfc61b66d02ce6f9b73b6fc38

Image Layers

1ADD file ... in / 72.57 MB
2LABEL org.label-schema.schema-version=1.0 org.label-schema.name=CentOS Base0 B
3CMD ["/bin/bash"]0 B
4ARG version0 B
5ARG bindir0 B
6ARG libdir0 B
7ARG trnascan_version0 B
8ARG ncbi_crisper_version0 B
9ARG prodigal_version0 B
10ARG pplacer_version0 B
11USER root0 B
12WORKDIR /root0 B
13COPY --chown=root:rootdir:212a1371d11ca59f14e070bf312733128fb17b7d1973c680464da431dac45c71 in /etc 1.05 KB
14|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18760 B
15|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18151.35 MB
16|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18101.07 MB
17|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18251.76 MB
18|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1810.61 MB
19|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18124.47 MB
20|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18203.87 MB
21|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18248.28 MB
22|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18106.41 MB
23|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a181.29 KB
24|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a185.01 MB
25|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1835.51 MB
26|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1838.84 MB
27|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1837.61 MB
28|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1871.39 MB
29COPY file:1704ef0fbbe5e868a888a21fd8d9fe507b5c1f5739eecdfab7d2fccd5ace9691 in /root/venv/lib/python3.9/site-packages/checkm/DATA_CONFIG 385 B
30ENV PGAP_VERSION=2023-05-17.build67710 B
31ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system0 B
32|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18256 B
33COPY file:af2cfb6ffb05b96510a1a2a11ce2a130db95a5d59e6d87d150d46944c8e2d240 in /root 12 MB
34COPY file:5f827efeb53bd6148c82fbfb980f13566aac86704e02d40c12b5e348f4a41003 in /root 2.54 MB
35COPY file:eb26204616f7bc18c589733a8cfec1cafdb5020e4f0968ac418f829cd2c725c6 in /root 29.96 MB
36WORKDIR /root0 B
37COPY dir:d83ef00b56ab1a7abde92f7a927f30bed58a444cb881cbf6037fd1cb213d5379 in /root/binaries 1.23 GB
38|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1812 MB
39|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a182.54 MB
40|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1829.96 MB
41WORKDIR /root/binaries0 B
42|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18887 MB
43|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1837.01 MB
44|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18262 B
45|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18319 B
46WORKDIR /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin0 B
47|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1851.87 MB
48WORKDIR /root0 B
49|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a182.28 KB
50ENV NCBI=/netopt/ncbi_tools640 B
51ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system0 B
52ENV PATH=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/third-party/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/hmmer/bin:/usr/local/prodigal/2.6.3/bin:/usr/local/pplacer/1.1a18/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
53ENV PATH=/root/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/third-party/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/hmmer/bin:/usr/local/prodigal/2.6.3/bin:/usr/local/pplacer/1.1a18/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
54ENV NI_SERVICE_NAME_TAXONOMY=some bogus value0 B
55ENV NI_SERVICE_NAME_TAXONOMY3=some bogus value0 B
56COPY dir:38870db4822069cf07d10dc6a5e04cb877575d502dcc9a26a87124217d709412 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin 108.97 MB
57COPY dir:92a61411e181d375cfd5980be6b96859d016c464d508b2b78fdc68bd85828348 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/third-party/arch/x86_64/bin 55.32 MB
58COPY file:5e88e86333eca3b2642c8f0550f7aaa43d93dd4a3d6ec8edaad8d0712f911fa5 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/ 341 B
59COPY multi:a7370b564333fc1d6d434f9de13ffd37c4b0827e418a26bc4f321377d3fc762d in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin/ 108.97 MB
60COPY file:027a04a8839caf6c1c066c5569f2f3c13b8e7427dc063ad78c237c5fe7874bd7 in /root 742 B
61|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18244.62 MB
62COPY multi:88ce6277b6f6b2207fb58fc31c54ef0afc5e1f8b5d3d59f9a5cf9643d117dbc0 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin/ 8.53 KB
63COPY multi:938ec9b55745c523210ced460f7b3ae305a3465bec777ce2ca1c1067f32a2c06 in /lib64/ 7.63 MB
64|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18200 B
65COPY file:43954742ab4272140c1db78047033c5688c793a779a1ace4199e82899b9630c0 in /opt/ncbi/64/lmdb-0.9.24/lib64/liblmdb.so 121.5 KB
66COPY file:3969a3de030a1e912e8aa87e0f0577e99e8a49b63a53aaa467d5a0358cba7287 in /netopt/ncbi_tools64/.ncbirc 629 B
67|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18131 B
68|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18277 B
69WORKDIR /home/gpipe0 B
70|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18232.73 MB
71CMD ["/usr/bin/bash"]0 B
72USER root0 B
73COPY dir:c7e7e1cbdd07528df2d126a0b48dea55c4412953dd291df83e04bf3ea7fcc0d0 in /pgap/pgap 38.23 MB
74WORKDIR /root0 B
75/bin/sh -c venv/bin/pip3 install -U394.8 KB
76/bin/sh -c venv/bin/pip3 install -U1.34 MB
77/bin/sh -c venv/bin/pip3 install -U34.28 KB
78/bin/sh -c venv/bin/pip3 install -U46.79 MB
79/bin/sh -c venv/bin/pip3 install -U4.88 KB
80/bin/sh -c chmod -R a+rx281.16 MB
81/bin/sh -c mkdir /pgap/input148 B
82WORKDIR /pgap0 B
83CMD ["/bin/sh"]0 B
84ARG PGAPX_BUILD0 B
85ARG PGAPX_REFDATA_BUCKET0 B
86ARG RAPT_BUILD0 B
87ENV PYTHONUNBUFFERED=10 B
88ENV NCBI=/netopt/ncbi_tools640 B
89ENV PATH=/root/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-05-17.build6771/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/third-party/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/hmmer/bin:/usr/local/prodigal/2.6.3/bin:/usr/local/pplacer/1.1a18/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/skesa:/usr/bin/vdb0 B
90ENV LD_LIBRARY_PATH=:/usr/lib/ngs:/usr/lib/vdb0 B
91COPY dir:c50d81cc0ae8bcc619cca10b10485bbf57cdad5e0117f18d60d6a3512a34d1dc in / 176.42 MB
92ENV PGAPX_BUILD=2023-05-17.build67710 B
93ENV RAPT_BUILD=rapt-456398940 B
94ENV PGAPX_REFDATA_BUCKET=ncbi-pgap-refdata0 B
95ENV TINI_VERSION=v0.19.00 B
96ADD 84b50f1acc38c999c313832de2ae4bbedb1f1fa3ab9c76209b6f0adee5230fd1 in /tini 9.24 KB
97/bin/sh -c chmod +x /tini9.24 KB
98ENTRYPOINT ["/tini" "--"]0 B
99CMD ["/app/execute"]0 B

Command

ADD file:b3ebbe8bd304723d43b7b44a6d990cd657b63d93d6a2a9293983a30bfc1dfa53 in /