Namespace
ncbi
Image / Tagpgap:2021-05-19.build5429
Content Digestsha256:9861891483233ae27f7c74eaa921792edd2eb1d36752c8dc722ca19efb984532
Details
2021-05-19 12:22:09 UTC
2.95 GB
Labels
-
org.label-schema.build-date20191001
-
org.label-schema.licenseGPLv2
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org.label-schema.nameCentOS Base Image
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org.label-schema.schema-version1.0
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org.label-schema.vendorCentOS
Environment
GP_HOME/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system
NCBI/netopt/ncbi_tools64
NI_SERVICE_NAME_TAXONOMY3some bogus value
NI_SERVICE_NAME_TAXONOMYsome bogus value
PATH/pgap/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PGAP_VERSION2021-05-19.build5429
Layers
[#000] sha256:ab5ef0e5819490abe86106fd9f4381123e37a03e80e650be39f7938d30ecb530 - 2.39% (72.3 MB)
[#001] sha256:bab1ad76a528ca6fa51dd0705678a35c84e9da8fd21dad1f12e6f32874710dea - 0.0% (1.01 KB)
[#002] sha256:888bdc3a11daab6780c0ff2ff39cc3299cd8c993a6380b594a4450c583274f61 - 0.0% (761 Bytes)
[#003] sha256:a581dbcd57692cb853833ed5263847f3c9fed8f6592dc50b2addf802a4475aff - 10.52% (318 MB)
[#004] sha256:eb5b428878d331b1b25767f6a2bf0b77e224823101f83d2be95cf43dd422588d - 0.36% (10.9 MB)
[#005] sha256:c855db0a5ebf2da42ac44cb1f753460c2ab8e48f69fc62b9c8997af04abde928 - 3.11% (94.1 MB)
[#006] sha256:f0b57f891e3f9d822a07189857261ef3f07d4b7539893816761df4620f08f35a - 5.74% (173 MB)
[#007] sha256:befac5d20be9910120e86c8926220c93b1fd9145fb2b26754d6462c2c16ad00b - 0.0% (1.29 KB)
[#008] sha256:e61d3611e24bdbfe29dce9b86befe2a93f584fa36626b3c4d5227179d6b9d78c - 0.0% (256 Bytes)
[#009] sha256:30fe32e4955d58e3242431663b11b5960f3d9e3d6bedd79f38839f2fd3721e88 - 1.82% (55 MB)
[#010] sha256:aae50dd0eb2e11cfeb90ed5439242f18158fb8eb16b966bd9655c4993a1c3ab9 - 35.57% (1.05 GB)
[#011] sha256:76622e2a5b1b34f7af1592f5ddbe4329fa47536bb7297ef756e14e9c72c00358 - 1.82% (55 MB)
[#012] sha256:5d5b91278ba6d2c76e2ac13d22b06cbeb821d6217c1a10a09f5728cb9275a7c2 - 22.88% (691 MB)
[#013] sha256:a469c2cb70c27f0257d67545b941b99add30117fa3138658fa3d2ee465a7a818 - 1.21% (36.6 MB)
[#014] sha256:9f36f6b5cdf90bbb5c9533a425fe411a346a172e26a68c9445d474080ec850f3 - 0.0% (265 Bytes)
[#015] sha256:a7ead4eb4e0c8722798991bdcdcda4f000d6d5a92b247de4cd23f2e6f91c9f2b - 0.0% (322 Bytes)
[#016] sha256:8b72aa48724f8105503133007b51ad65145ddcb1ba39ba1eb1cf937545095ecd - 4.53% (137 MB)
[#017] sha256:a2ca4b11c1287309f3b6b82b1e8373559b0ecd365657b712df28bb91c2bd4ec2 - 0.0% (2.27 KB)
[#018] sha256:599c6c61b026d83a8b8138f5cbe1307ff9dd76c29acf0218790b0ea0af19e2ab - 3.68% (111 MB)
[#019] sha256:2c7d641630474a8b2349b3ff9ddea09cbea51864d6d17433c86047d98eb289a1 - 0.0% (321 Bytes)
[#020] sha256:ae0f24bdc7e3b49637eb2478755d29f92c148b6cf3ab02c74b0835cb07ff7827 - 3.68% (111 MB)
[#021] sha256:12b8f292deee915e9da3d9987cd1c88f58eb930ef729cb9258db814d13c95160 - 0.0% (8.24 KB)
[#022] sha256:4ebc2ad253af866f73ca662f1c0ca0ee782db8057c8ac52be2435d6c876810cf - 0.21% (6.24 MB)
[#023] sha256:be7d4b3380f91a67404c8e58195aad7ad48a2c15da229e409a6b74bd6d6612e9 - 0.0% (633 Bytes)
[#024] sha256:7d8f76be6c0c1709c00023e4bf489b32898e8816c3f01aeae63287f0aa552b9a - 0.0% (131 Bytes)
[#025] sha256:dafa9a415615f0fb9685f2331cad3074db798fc6de8105c42562cf590a2ed0c0 - 1.21% (36.6 MB)
[#026] sha256:0d5392197225efdf5ad83f56580f2e0357a5d05d106896a6c5913ae3ea380e58 - 0.1% (3.15 MB)
[#027] sha256:9d6f0bbb186034ee3296bd80204bec4885eb534d56ba40000fa7df1324664cb9 - 0.04% (1.25 MB)
[#028] sha256:d7a0103c161b2514592c57477852d3f8c132ad2a66b72db3edb22044e8c63924 - 1.08% (32.6 MB)
[#029] sha256:fbedd34aa0ffb913347a3c750850a32e8b1f508f52315b23203f198be155f608 - 0.0% (4.39 KB)
[#030] sha256:0a132ef04d14254389fc876eb751cec9b1da82569b2da7cfa7872c3385df86dd - 0.03% (983 KB)
[#031] sha256:657cbcde2653c844bfc7c9a9e4b913606cc69a9fc487b85ab506bf1cdda7b16f - 0.0% (148 Bytes)
History
/bin/sh -c #(nop) ADD file:45a381049c52b5664e5e911dead277b25fadbae689c0bb35be3c42dff0f2dffe in /
2019-11-12 00:20:33 UTC/bin/sh -c #(nop) LABEL org.label-schema.schema-version=1.0 org.label-schema.name=CentOS Base Image org.label-schema.vendor=CentOS org.label-schema.license=GPLv2 org.label-schema.build-date=20191001
2019-11-12 00:20:33 UTC/bin/sh -c #(nop) CMD ["/bin/bash"]
2020-04-15 11:16:53 UTC/bin/sh -c #(nop) ARG version
2020-04-15 11:16:54 UTC/bin/sh -c #(nop) ARG bindir
2020-04-15 11:16:55 UTC/bin/sh -c #(nop) ARG libdir
2020-04-15 11:16:56 UTC/bin/sh -c #(nop) ARG trnascan_version
2020-04-15 11:16:57 UTC/bin/sh -c #(nop) ARG ncbi_crisper_version
2020-04-15 11:16:58 UTC/bin/sh -c #(nop) USER root
2020-04-15 11:17:00 UTC/bin/sh -c #(nop) WORKDIR /root
2021-03-18 14:49:00 UTC/bin/sh -c #(nop) COPY --chown=root:rootdir:826106db113e3da347bb06feb4a923d0c11a45440c5154323248b248566809b3 in /etc
2021-05-19 11:09:35 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c echo "ip_resolve=4" >> /etc/yum.conf
2021-05-19 11:18:27 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c yum -y update && yum -y install yum-utils && yum -y groupinstall development
2021-05-19 11:18:48 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c yum -y install https://repo.ius.io/ius-release-el7.rpm https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
2021-05-19 11:19:29 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c yum -y install ncbi-python37 nodejs
2021-05-19 11:22:21 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c yum -y install binutils perl sqlite ncbi-crispr${ncbi_crisper_version} nodejs ncbi-gcc730-opt-libs ncbi-gcc493-opt-libs PyYAML
2021-05-19 11:22:35 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c ln -s /usr/bin/perl /usr/bin/perl5.16 && ln -s /usr/bin/perl /opt/perl/5.16.3/bin/perl && ln -s /usr/bin/node /usr/bin/nodejs && rm /etc/yum.repos.d/ncbi.repo && echo -e "* soft nofile 8192\n* hard nofile 8192\n" >> /etc/security/limits.conf
2021-05-19 11:22:43 UTC/bin/sh -c #(nop) ENV PGAP_VERSION=2021-05-19.build5429
2021-05-19 11:22:52 UTC/bin/sh -c #(nop) ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system
2021-05-19 11:23:05 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c mkdir -p ${GP_HOME} && ln -s /panfs/pan1.be-md.ncbi.nlm.nih.gov /panfs/pan1
2021-05-19 11:23:12 UTC/bin/sh -c #(nop) COPY file:aeb6727cb3ff81a24840e275d624d2d92025995375afe628c530fa6da984fb9b in /root
2021-05-19 11:23:23 UTC/bin/sh -c #(nop) WORKDIR /root
2021-05-19 11:24:06 UTC/bin/sh -c #(nop) COPY dir:0c0ee43e3ea983d05df607455f417313ce9a663664639ccfd172eb29bcd5eb36 in /root/binaries
2021-05-19 11:24:25 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c tar xvPf infernal.tgz -C /
2021-05-19 11:24:38 UTC/bin/sh -c #(nop) WORKDIR /root/binaries
2021-05-19 11:26:27 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c tar --exclude='*/etc' --exclude='*/setup' --exclude='*/src.tar.gz' -xvf install.tar.gz -C /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system && tar xvPf linked_exe.tar -C / && tar xvPf libraries.tar -C / --skip-old-files && tar xvPf trnascan.tgz -C /
2021-05-19 11:26:51 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c mkdir /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ThirdParty/GeneMark && cd /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ThirdParty/GeneMark && tar xvf /root/binaries/genemark.tgz
2021-05-19 11:27:04 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c cd /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ThirdParty/tRNAscan-SE/ && rm -rf production && ln -s ${trnascan_version} production
2021-05-19 11:27:17 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c mv ${GP_HOME}/next ${GP_HOME}/current && ln -s ${GP_HOME}/current/arch/x86_64/bin ${GP_HOME}/bin
2021-05-19 11:27:27 UTC/bin/sh -c #(nop) WORKDIR /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin
2021-05-19 11:27:52 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c find . -maxdepth 1 -type f -not -name "*.p*" -not -name "*.txt" -not -name "*.ini" -not -name "cluster_blastp_wnode" -print0 | xargs -0 -i strip {}
2021-05-19 11:28:03 UTC/bin/sh -c #(nop) WORKDIR /root
2021-05-19 11:28:16 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c useradd -ms /bin/bash gpipe
2021-05-19 11:28:25 UTC/bin/sh -c #(nop) ENV NCBI=/netopt/ncbi_tools64
2021-05-19 11:28:34 UTC/bin/sh -c #(nop) ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system
2021-05-19 11:28:42 UTC/bin/sh -c #(nop) ENV PATH=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
2021-05-19 11:28:52 UTC/bin/sh -c #(nop) ENV NI_SERVICE_NAME_TAXONOMY=some bogus value
2021-05-19 11:29:01 UTC/bin/sh -c #(nop) ENV NI_SERVICE_NAME_TAXONOMY3=some bogus value
2021-05-19 11:29:13 UTC/bin/sh -c #(nop) COPY dir:8bff0b74d4a9a35b2235d8fe7d0bb3aa1a10541535232727e4fd4ff69a05dcaa in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin
2021-05-19 11:29:17 UTC/bin/sh -c #(nop) COPY file:196badb475cb8d8d075c4d5c7f92fa6d88b73f4dfc241d5f46e6660815fa7726 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/
2021-05-19 11:29:32 UTC/bin/sh -c #(nop) COPY multi:5b43ed9fbc838050b84aa2a5e605720dd96ce509d89b60aa98fb8fe97938e2fb in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin/
2021-05-19 11:29:40 UTC/bin/sh -c #(nop) COPY multi:c129b80ff25c7de8f8d0b22d56ab7d70c10574aa4c14001f697c39c0eb866581 in /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin/
2021-05-19 11:29:43 UTC/bin/sh -c #(nop) COPY multi:f8150279596baa1727b51d7a208165254e1726b7b8d05490f850c7be5892a419 in /lib64/
2021-05-19 11:29:46 UTC/bin/sh -c #(nop) COPY file:3969a3de030a1e912e8aa87e0f0577e99e8a49b63a53aaa467d5a0358cba7287 in /netopt/ncbi_tools64/.ncbirc
2021-05-19 11:29:58 UTC|5 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/lib ncbi_crisper_version=1.02 trnascan_version=2.0.7 version=2021-05-19.build5429 /bin/sh -c rm -rf binaries
2021-05-19 11:30:10 UTC/bin/sh -c #(nop) WORKDIR /home/gpipe
2021-05-19 11:30:19 UTC/bin/sh -c #(nop) CMD ["/usr/bin/bash"]
2021-05-19 12:20:58 UTC/bin/sh -c #(nop) USER root
2021-05-19 12:21:06 UTC/bin/sh -c #(nop) COPY dir:39efaf82455ad8281e5b56bdb8bc3c952d4e79a83b6a9acde7a6eb9e99342522 in /pgap/pgap
2021-05-19 12:21:09 UTC/bin/sh -c #(nop) WORKDIR /pgap
2021-05-19 12:21:20 UTC/bin/sh -c /opt/python-3.7/bin/python3.7 -m venv venv
2021-05-19 12:21:24 UTC/bin/sh -c venv/bin/pip3 install -U PyYAML
2021-05-19 12:21:52 UTC/bin/sh -c venv/bin/pip3 install -U cwltool[deps]==3.0.20210124104916
2021-05-19 12:21:58 UTC/bin/sh -c venv/bin/pip3 install -U cwlref-runner
2021-05-19 12:22:03 UTC/bin/sh -c venv/bin/pip3 install -U schema-salad==7.1.20210309094900
2021-05-19 12:22:05 UTC/bin/sh -c #(nop) ENV PATH=/pgap/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-05-19.build5429/arch/x86_64/bin:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
2021-05-19 12:22:07 UTC/bin/sh -c mkdir /pgap/input
2021-05-19 12:22:09 UTC/bin/sh -c #(nop) CMD ["/bin/sh"]
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