Namespace
ncbi
Image / Tagpgap:2024-04-27.build7426
Content Digestsha256:18241c03063a6cacfe96b5938578c664934c6cd984af55eec78766646a9481b9
Details
2024-04-27 14:02:33 -0400
4.2 GB
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/root/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/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
PGAP_VERSION2024-04-27.build7426
Layers
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[#004] sha256:eeecee02596378a7ea6ce078d62c0c86e9d06443a7bf46e9724e01387e1966bf - 3.06% (131 MB)
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[#006] sha256:dde5a967f72e1ff7156ae9225e8c79d3bd7c3b8521b87da4ac7b079a8f9c8b39 - 8.43% (362 MB)
[#007] sha256:0dbffbd4008a453dc69f50be7b7d0a59275a1cc8875a57698a892ff4674f17e7 - 0.29% (12.6 MB)
[#008] sha256:169c263fe1ae4257aafcd883748ade1b0e8d0ddae5197c2c4a24c70ad694c066 - 1.08% (46.4 MB)
[#009] sha256:f237a260458f34f08c914d5ad6d7eb059a8397ae7846dffebf437a404e00be5f - 0.93% (40 MB)
[#010] sha256:b74079ebbde10a313e01c9d157599c58856e627c717c4329ea2d3a58e6b4b48d - 0.27% (11.7 MB)
[#011] sha256:9569923f29ab85962ca7e4783706275669c816d7ca7f3c8d377a7e8ef66f924d - 0.57% (24.4 MB)
[#012] sha256:8942da87dd08a5f8c7390472e56e5f9589d8d7a8d0347ecf3feab5d50005ba67 - 0.0% (1.18 KB)
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[#014] sha256:225407b33c735755c1ed089c09d67329c1570197f7951bf0cfec8a23fc6c8901 - 0.87% (37.4 MB)
[#015] sha256:53ac52c9fc6957968ea636728002bfa08742bc7ea5eebb82a2aa21a5b5ea1699 - 1.13% (48.5 MB)
[#016] sha256:d982cfe858d3f4299b8e5a109ac8f5130f8200c9cc13970e011b3e4eead715b8 - 1.07% (46.1 MB)
[#017] sha256:f1f2c2293a7961a4031556aa516ab96bf5f09040aedea6d8f2a5db71c5bcc661 - 1.86% (79.9 MB)
[#018] sha256:73e5b86312079dce476ef544d41b95026a7c379cb5539c197df7c6e0e837f87b - 0.0% (387 Bytes)
[#019] sha256:400ed96da694dd8d154690ee666f78ec8f47a870677503be5999b2e69930e3a0 - 0.0% (253 Bytes)
[#020] sha256:aab90a0f75055401f6a15be283f7b9e6dc3f014ab9a6345112a76e4e04922ac2 - 0.29% (12.3 MB)
[#021] sha256:f75b7978159576b68b5b2508b105cc62aa53feca3bde147d68f202bcbacdba7a - 0.06% (2.54 MB)
[#022] sha256:3437664554e6fd7cb0d71885f61ab5490249868d3b5e7435d9fe237d071f6ccd - 0.23% (9.98 MB)
[#023] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#024] sha256:951a90f6828ef15659fe602ead505651304528f460bfdbfe0eefb93c74a5819c - 31.42% (1.32 GB)
[#025] sha256:dde4eb7c9286b4b1a3171325c26da7b9bbfb85e4958487ecf0b04344b894058a - 0.29% (12.3 MB)
[#026] sha256:f3dc915a7ff7e125c0977e56ace7d4cc0b0730dce6b10eb8ee75a467acdcd9e3 - 0.06% (2.54 MB)
[#027] sha256:a931876d530583c68c14ccffaf22116a28ecbe3961d9bcf846050c5b1399c768 - 0.23% (9.98 MB)
[#028] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#029] sha256:41ddd0766facaa22af63a9005432b3ed835e155201c0f064e7ab84ff47556e61 - 18.18% (782 MB)
[#030] sha256:0c0c62670abe0b469e0d08cbe349044bf72d7b3fc9825f3ad4e007b825168316 - 0.86% (37 MB)
[#031] sha256:f5c5142da6240fa261676e3f1b480b4c8b4280c0f58a7b73d4f470d2dbdb03cc - 0.0% (246 Bytes)
[#032] sha256:5027ea4491d59544ada17808f26e6e571357b0d8df2b10dcf9e8b514b2374140 - 0.0% (205 Bytes)
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[#034] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#035] sha256:f89b7d09c37eedbc396a5286cccbd3c52b661c8e74de5a76753f751db666973d - 1.29% (55.2 MB)
[#036] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#037] sha256:0875bdb8c8594bcb86a65b676f32d9d51050ca992df2693efa6b0dca1b0e2714 - 0.0% (1.78 KB)
[#038] sha256:e5926e1f506c22bc974b3b8071a4f75aeb17de438d2d89d02d1c5c642857c44a - 3.69% (159 MB)
[#039] sha256:bd842d2bfe53dce3d38f81c8075abc2006557a842658bc081109378801b58c97 - 1.39% (59.6 MB)
[#040] sha256:e902fee6c5cbc0d2b086ace9b8ec03d09c166cc7c38336d50bd8a2f0f89a89ce - 0.0% (341 Bytes)
[#041] sha256:bc0992c7b648a72117c3ee22eb4a96b145462529e6de4fec7d0dd9d3e0470372 - 3.69% (159 MB)
[#042] sha256:c5c5062ef91cd36cd2d6e58f1dbdb821dc6dd9ca5c6b4810d1cdefaa659205c0 - 0.0% (741 Bytes)
[#043] sha256:aec3eef22b3e03eac970f97e0ea230512ab175155b4798b84c1acab6b2177146 - 2.91% (125 MB)
[#044] sha256:7c9a04a23cd9f117a3d242914bce65655a9b8ab3b10164be5a00edd6a4089283 - 0.0% (8.66 KB)
[#045] sha256:c85fc2c853bc2534c7cda12c27cfea313a43ec4c6130e7ef94c9babd288af201 - 0.0% (259 Bytes)
[#046] sha256:eae474e6e00a387a58bf8db26cd047030c232b2f063dd800672e6934857c0427 - 0.0% (48.2 KB)
[#047] sha256:1b80767391ac0b327045e9c112f8f6df0b79a8dfc52afa48ff49d1e817caa312 - 0.03% (1.08 MB)
[#048] sha256:6e33757e2b887121a0ed88cedfd63ffd0d0537ad5ce8fbd7a34cae3ca42f4787 - 0.0% (631 Bytes)
[#049] sha256:b17dde468b0e926d2c7795db62ee64a0f77dbdd97b58890b278306c72d732803 - 0.0% (131 Bytes)
[#050] sha256:c520d70e9810472f8224dd01baad37f55b06265335155f516de33c345c0533cf - 0.0% (277 Bytes)
[#051] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#052] sha256:cc0b823959a8cf2906344c9865d6a43cdcbf179285bcbb687b7b2a165391d5c6 - 5.62% (241 MB)
[#053] sha256:97c5697f34a6ccedd6790c4055f161315c9ae6f3b661d498526e14d83b43f319 - 0.89% (38.2 MB)
[#054] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#055] sha256:d0a5d14b46fc10adb395f222bce93dd4436fd317d22369e4eb224af7743bf3c0 - 0.01% (411 KB)
[#056] sha256:5944092ae6114b42e7104c55a7ba1280a52ecf9d38b1291a6554b1825cd44b53 - 0.04% (1.51 MB)
[#057] sha256:415d7e107cff8153712f7bd4b6b27b38fba66cae190b778b2d9eaf4b502ff975 - 0.0% (43.4 KB)
[#058] sha256:76e432afbcdb041a65295baf7f1e39de2d595d789056591bd965a33be4f3196b - 0.9% (38.7 MB)
[#059] sha256:08996f858bba74f62c77f6c57952bb8e220ec5ff126a7daadfae54aec39b3162 - 0.0% (5.32 KB)
[#060] sha256:5fdbb5c311784aca6f08232c1df04f2248d96625e0d374def32b0b423e8cab39 - 6.56% (282 MB)
[#061] sha256:8ac6645988d8f31d45d871d98858290943516535ef01c4fa8e5e6b7a26dc8b48 - 0.0% (146 Bytes)
[#062] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
History
/bin/sh -c #(nop) ADD file:610f0f89947b77888b5ea9c8578305ef1d1ca0ec526e48d5f64967200e4c8f39 in /
2023-11-28 23:28:03 UTC/bin/sh -c #(nop) CMD ["/bin/bash"]
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG version
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG bindir
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG libdir
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG trnascan_version
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG ncbi_crisper_version
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG prodigal_version
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)ARG pplacer_version
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)USER root
2024-04-18 12:59:46 -0400 (buildkit.dockerfile.v0)WORKDIR /root
2024-04-18 12:59:51 -0400 (buildkit.dockerfile.v0)COPY --chown=root:root etc /etc # buildkit
2024-04-27 13:32:14 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c echo "ip_resolve=4" >> /etc/yum.conf # buildkit
2024-04-27 13:32:34 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum -y update -v # buildkit
2024-04-27 13:32:36 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum -y install yum-utils # buildkit
2024-04-27 13:33:21 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum -y groupinstall development # buildkit
2024-04-27 13:33:23 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /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 # buildkit
2024-04-27 13:33:41 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum -y install ncbi-python39 nodejs # buildkit
2024-04-27 13:33:45 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum -y install binutils perl sqlite ncbi-crispr${ncbi_crisper_version} nodejs ncbi-gcc730-opt-libs ncbi-gcc493-opt-libs python3-pyyaml # buildkit
2024-04-27 13:33:47 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum makecache # buildkit
2024-04-27 13:33:49 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c yum -y install bzip2-devel xz-devel zlib-devel # buildkit
2024-04-27 13:33:51 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c 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 # buildkit
2024-04-27 13:33:54 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c /opt/python-3.9/bin/python3.9 -m venv venv # buildkit
2024-04-27 13:33:58 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c venv/bin/pip3 install -U numpy # buildkit
2024-04-27 13:34:03 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c venv/bin/pip3 install -U matplotlib # buildkit
2024-04-27 13:34:05 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c venv/bin/pip3 install -U pysam # buildkit
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c venv/bin/pip3 install -U checkm-genome # buildkit
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)COPY DATA_CONFIG /root/venv/lib/python3.9/site-packages/checkm/DATA_CONFIG # buildkit
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)ENV PGAP_VERSION=2024-04-27.build7426
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c mkdir -p ${GP_HOME} && ln -s /panfs/pan1.be-md.ncbi.nlm.nih.gov /panfs/pan1 # buildkit
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)COPY infernal.tgz /root # buildkit
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)COPY prodigal.tgz /root # buildkit
2024-04-27 13:34:10 -0400 (buildkit.dockerfile.v0)COPY pplacer.tgz /root # buildkit
2024-04-27 13:34:11 -0400 (buildkit.dockerfile.v0)WORKDIR /root
2024-04-27 13:34:13 -0400 (buildkit.dockerfile.v0)COPY binaries /root/binaries # buildkit
2024-04-27 13:34:14 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c tar xvPf infernal.tgz -C / # buildkit
2024-04-27 13:34:15 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c tar xvPf prodigal.tgz -C / # buildkit
2024-04-27 13:34:15 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c tar xvPf pplacer.tgz -C / # buildkit
2024-04-27 13:34:15 -0400 (buildkit.dockerfile.v0)WORKDIR /root/binaries
2024-04-27 13:34:32 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /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 / # buildkit
2024-04-27 13:34:35 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c mkdir /netmnt/vast01/gp/ThirdParty/GeneMark && cd /netmnt/vast01/gp/ThirdParty/GeneMark && tar xvf /root/binaries/genemark.tgz # buildkit
2024-04-27 13:34:35 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c cd /netmnt/vast01/gp/ThirdParty/tRNAscan-SE && rm -rf production && ln -s ${trnascan_version} production # buildkit
2024-04-27 13:34:35 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c ln -s /netmnt/vast01/gp/ThirdParty /panfs/pan1/gpipe/ThirdParty # buildkit
2024-04-27 13:34:36 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c mv ${GP_HOME}/next ${GP_HOME}/current && ln -s ${GP_HOME}/current/arch/x86_64/bin ${GP_HOME}/bin # buildkit
2024-04-27 13:34:37 -0400 (buildkit.dockerfile.v0)WORKDIR /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /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 {} # buildkit
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)WORKDIR /root
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c useradd -ms /bin/bash gpipe # buildkit
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)ENV NCBI=/netopt/ncbi_tools64
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)ENV GP_HOME=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)ENV PATH=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/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
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)ENV PATH=/root/venv/bin/:/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/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
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)ENV NI_SERVICE_NAME_TAXONOMY=some bogus value
2024-04-27 13:34:40 -0400 (buildkit.dockerfile.v0)ENV NI_SERVICE_NAME_TAXONOMY3=some bogus value
2024-04-27 13:34:41 -0400 (buildkit.dockerfile.v0)COPY binaries/bin /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin # buildkit
2024-04-27 13:34:41 -0400 (buildkit.dockerfile.v0)COPY binaries/third-party-bin /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/third-party/arch/x86_64/bin # buildkit
2024-04-27 13:34:41 -0400 (buildkit.dockerfile.v0)COPY package.versions /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/ # buildkit
2024-04-27 13:34:42 -0400 (buildkit.dockerfile.v0)COPY binaries/bin/* /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin/ # buildkit
2024-04-27 13:34:42 -0400 (buildkit.dockerfile.v0)COPY ./cleanup_image.sh /root # buildkit
2024-04-27 13:34:43 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c ./cleanup_image.sh # buildkit
2024-04-27 13:34:43 -0400 (buildkit.dockerfile.v0)COPY scripts/* /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin/ # buildkit
2024-04-27 13:34:44 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c mkdir -p /opt/ncbi/64/lmdb-0.9.24/lib64/ /opt/ncbi/gcc/12.2.0/lib64/ # buildkit
2024-04-27 13:34:44 -0400 (buildkit.dockerfile.v0)COPY liblmdb.so /opt/ncbi/64/lmdb-0.9.24/lib64/liblmdb.so # buildkit
2024-04-27 13:34:44 -0400 (buildkit.dockerfile.v0)COPY libstdc++.so.6 libgcc_s.so.1 libgomp.so.1 /opt/ncbi/gcc/12.2.0/lib64/ # buildkit
2024-04-27 13:34:44 -0400 (buildkit.dockerfile.v0)COPY ncbirc /netopt/ncbi_tools64/.ncbirc # buildkit
2024-04-27 13:34:44 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c rm -rf binaries # buildkit
2024-04-27 13:34:45 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c echo 'export PS1="$ "' >> /root/.bash_profile # buildkit
2024-04-27 13:34:45 -0400 (buildkit.dockerfile.v0)WORKDIR /home/gpipe
2024-04-27 13:34:48 -0400 (buildkit.dockerfile.v0)RUN |7 version=2024-04-27.build7426 bindir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/bin libdir=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2024-04-27.build7426/arch/x86_64/lib trnascan_version=2.0.12 ncbi_crisper_version=1.03 prodigal_version=2.6.3 pplacer_version=1.1a18 /bin/sh -c chmod -R a+rx /root/ # buildkit
2024-04-27 13:34:48 -0400 (buildkit.dockerfile.v0)CMD ["/usr/bin/bash"]
2024-04-27 14:02:05 -0400 (buildkit.dockerfile.v0)USER root
2024-04-27 14:02:05 -0400 (buildkit.dockerfile.v0)COPY pgap /pgap/pgap # buildkit
2024-04-27 14:02:05 -0400 (buildkit.dockerfile.v0)WORKDIR /root
2024-04-27 14:02:08 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c venv/bin/pip3 install -U 'urllib3<2' # buildkit
2024-04-27 14:02:10 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c venv/bin/pip3 install -U PyYAML # buildkit
2024-04-27 14:02:11 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c venv/bin/pip3 install -U filelock # buildkit
2024-04-27 14:02:22 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c venv/bin/pip3 install -U cwltool[deps]==3.1.20230513155734 # buildkit
2024-04-27 14:02:24 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c venv/bin/pip3 install -U cwlref-runner # buildkit
2024-04-27 14:02:33 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c chmod -R a+rx /root/ # buildkit
2024-04-27 14:02:33 -0400 (buildkit.dockerfile.v0)RUN /bin/sh -c mkdir /pgap/input # buildkit
2024-04-27 14:02:33 -0400 (buildkit.dockerfile.v0)WORKDIR /pgap
2024-04-27 14:02:33 -0400 (buildkit.dockerfile.v0)CMD ["/bin/sh"]
Delete Tag
Please be careful as this will not just delete the reference but also the actual content!
For example when you have latest and v1.2.3 both pointing to the same image
the deletion of latest will also permanently remove v1.2.3.