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ncbi/rapt:v0.5.4

Manifest digest

sha256:6992ea88a7b8475bad0d1eece0634163bc8d4e890e96886eb9e608ba17d44a22

OS/ARCH

linux/amd64

Compressed size

4.91 GB

Last pushed

over 2 years by gpipe

Type

Image

Manifest digest

sha256:6992ea88a7b8475bad0d1eece0634163bc8d4e890e96886eb9e608ba17d44a22

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:8e7d04b988c54c0db41d5bfaa5a828be2dd546d043d1a28f2d7f0d997c29d856 in /etc 1 KB
14|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/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/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18331.71 MB
16|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1810.92 MB
17|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18116.15 MB
18|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18195.57 MB
19|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18233.32 MB
20|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1898.07 MB
21|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a181.3 KB
22|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a185.01 MB
23|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1835.01 MB
24|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1838.62 MB
25|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1813.39 MB
26|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18103.3 MB
27COPY file:1704ef0fbbe5e868a888a21fd8d9fe507b5c1f5739eecdfab7d2fccd5ace9691 in /root/venv/lib/python3.9/site-packages/checkm/DATA_CONFIG 386 B
28ENV PGAP_VERSION=2022-10-03.build63840 B
29ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system0 B
30|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18256 B
31COPY file:aeb6727cb3ff81a24840e275d624d2d92025995375afe628c530fa6da984fb9b in /root 55.03 MB
32COPY file:5f827efeb53bd6148c82fbfb980f13566aac86704e02d40c12b5e348f4a41003 in /root 2.54 MB
33COPY file:eb26204616f7bc18c589733a8cfec1cafdb5020e4f0968ac418f829cd2c725c6 in /root 29.96 MB
34WORKDIR /root0 B
35COPY dir:b36eb46423ac48ae4175d5adb057551ea3df44f571e032b6cbc1670240fe5271 in /root/binaries 1.3 GB
36|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1855.03 MB
37|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a182.54 MB
38|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1829.96 MB
39WORKDIR /root/binaries0 B
40|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18948.59 MB
41|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a1837.01 MB
42|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18267 B
43|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18323 B
44WORKDIR /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin0 B
45|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18139.99 MB
46WORKDIR /root0 B
47|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a182.28 KB
48ENV NCBI=/netopt/ncbi_tools640 B
49ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system0 B
50ENV PATH=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/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
51ENV PATH=/root/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/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
52ENV NI_SERVICE_NAME_TAXONOMY=some bogus value0 B
53ENV NI_SERVICE_NAME_TAXONOMY3=some bogus value0 B
54COPY dir:86806a54dcedfcd5b096e37b58be90d1595d6244d10c75996de49d414e774e3b in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin 111.19 MB
55COPY file:2cacdbb4f5285b69048420cf773a673f8ed4f6cb85875a50bd2ea83219275761 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/ 345 B
56COPY multi:ac25b9f2c4e47081200b2fa192ff78b53ec090947636702c7f4df559877bc46d in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin/ 111.19 MB
57COPY multi:d04bda76af7537017840870bcc4338f238bdbc6727d94c44b85460a3ab57fdb5 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin/ 8.27 KB
58COPY multi:938ec9b55745c523210ced460f7b3ae305a3465bec777ce2ca1c1067f32a2c06 in /lib64/ 7.63 MB
59COPY file:3969a3de030a1e912e8aa87e0f0577e99e8a49b63a53aaa467d5a0358cba7287 in /netopt/ncbi_tools64/.ncbirc 632 B
60|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18131 B
61|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18278 B
62WORKDIR /home/gpipe0 B
63|7 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/arch/x86_64/lib ncbi_crisper_version=1.02 pplacer_version=1.1a18282.73 MB
64CMD ["/usr/bin/bash"]0 B
65USER root0 B
66COPY dir:33b26d7c037b0c5dc3130e5cf46e05dcbb45282211228c0a6e1e409528aa7a72 in /pgap/pgap 36.59 MB
67WORKDIR /root0 B
68/bin/sh -c venv/bin/pip3 install -U1.34 MB
69/bin/sh -c venv/bin/pip3 install -U28.91 KB
70/bin/sh -c venv/bin/pip3 install -U65.45 MB
71/bin/sh -c venv/bin/pip3 install -U4.69 KB
72/bin/sh -c chmod -R a+rx349.54 MB
73/bin/sh -c mkdir /pgap/input148 B
74WORKDIR /pgap0 B
75CMD ["/bin/sh"]0 B
76ARG PGAPX_BUILD0 B
77ARG PGAPX_REFDATA_BUCKET0 B
78ARG RAPT_BUILD0 B
79ENV PYTHONUNBUFFERED=10 B
80ENV NCBI=/netopt/ncbi_tools640 B
81ENV PATH=/root/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-10-03.build6384/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
82ENV LD_LIBRARY_PATH=:/usr/lib/ngs:/usr/lib/vdb0 B
83COPY dir:0b64346dd1e4a85c789a3f9c4409c5a6c2567b7a18e4cfbfdbfcda2e21f5a0bb in / 176.73 MB
84ENV PGAPX_BUILD=2022-10-03.build63840 B
85ENV RAPT_BUILD=rapt-415891820 B
86ENV PGAPX_REFDATA_BUCKET=ncbi-pgap-refdata0 B
87ENV TINI_VERSION=v0.19.00 B
88ADD 84b50f1acc38c999c313832de2ae4bbedb1f1fa3ab9c76209b6f0adee5230fd1 in /tini 9.24 KB
89/bin/sh -c chmod +x /tini9.24 KB
90ENTRYPOINT ["/tini" "--"]0 B
91CMD ["/app/execute"]0 B

Command

ADD file:b3ebbe8bd304723d43b7b44a6d990cd657b63d93d6a2a9293983a30bfc1dfa53 in /