The antibody-2019 from gifford-lab

Something wrong with Dockerfile building.

Hi,
There is something wrong when building Dockerfile.
This is my docker version.

Docker version 19.03.12, build 48a66213fe

And wrong message below

Sending build context to Docker daemon  3.584kB
Step 1/6 : FROM registry.codeocean.com/codeocean/tensorflow:1.4.0-python2.7.12-cuda8.0.61-cudnn6.0.21-ubuntu16.04
 ---> cbfaffda1e3e
Step 2/6 : ARG DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> d25e9a0680d8
Step 3/6 : RUN apt-get update     && apt-get install -y --no-install-recommends       "git-all=1:2.7.4-0ubuntu1.6"       "openssh-client=1:7.2p2-4ubuntu2.6"       "screen=4.3.1-2build1"       "sshpass=1.05-1"       "vim=2:7.4.1689-3ubuntu1.2"       "wget=1.17.1-1ubuntu1.4"     && rm -rf /var/lib/apt/lists/*
 ---> Running in b941f596736c
Get:1 http://storage.googleapis.com/bazel-apt stable InRelease [2256 B]
Ign:1 http://storage.googleapis.com/bazel-apt stable InRelease
Get:2 http://storage.googleapis.com/bazel-apt stable/jdk1.8 amd64 Packages [5219 B]
Ign:3 http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64  InRelease
Get:4 http://security.ubuntu.com/ubuntu xenial-security InRelease [109 kB]
Get:5 http://archive.ubuntu.com/ubuntu xenial InRelease [247 kB]
Ign:6 http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64  InRelease
Get:7 http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64  Release [697 B]
Get:8 http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64  Release [564 B]
Get:9 http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64  Release.gpg [836 B]
Get:10 http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64  Release.gpg [833 B]
Ign:11 http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64  Packages
Get:12 http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64  Packages [105 kB]
Get:13 http://security.ubuntu.com/ubuntu xenial-security/universe Sources [243 kB]
Get:14 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]
Get:11 http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64  Packages [398 kB]
Get:15 http://archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB]
Get:16 http://archive.ubuntu.com/ubuntu xenial/universe Sources [9802 kB]
Get:17 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [1839 kB]
Get:18 http://security.ubuntu.com/ubuntu xenial-security/restricted amd64 Packages [15.9 kB]
Get:19 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 Packages [968 kB]
Get:20 http://security.ubuntu.com/ubuntu xenial-security/multiverse amd64 Packages [9249 B]
Get:21 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages [1558 kB]
Get:22 http://archive.ubuntu.com/ubuntu xenial/restricted amd64 Packages [14.1 kB]
Get:23 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages [9827 kB]
Get:24 http://archive.ubuntu.com/ubuntu xenial/multiverse amd64 Packages [176 kB]
Get:25 http://archive.ubuntu.com/ubuntu xenial-updates/universe Sources [532 kB]
Get:26 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [2353 kB]
Get:27 http://archive.ubuntu.com/ubuntu xenial-updates/restricted amd64 Packages [16.4 kB]
Get:28 http://archive.ubuntu.com/ubuntu xenial-updates/universe amd64 Packages [1511 kB]
Get:29 http://archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 Packages [26.7 kB]
Get:30 http://archive.ubuntu.com/ubuntu xenial-backports/main amd64 Packages [10.9 kB]
Get:31 http://archive.ubuntu.com/ubuntu xenial-backports/universe amd64 Packages [12.6 kB]
Fetched 30.0 MB in 43s (689 kB/s)
Reading package lists...
W: GPG error: http://storage.googleapis.com/bazel-apt stable InRelease: The following signatures were invalid: KEYEXPIRED 1527185977  KEYEXPIRED 1527185977  KEYEXPIRED 1527185977
W: The repository 'http://storage.googleapis.com/bazel-apt stable InRelease' is not signed.
Reading package lists...
Building dependency tree...
Reading state information...
E: Version '1:2.7.4-0ubuntu1.6' for 'git-all' was not found
E: Version '1:7.2p2-4ubuntu2.6' for 'openssh-client' was not found
E: Version '2:7.4.1689-3ubuntu1.2' for 'vim' was not found
E: Version '1.17.1-1ubuntu1.4' for 'wget' was not found
The command '/bin/sh -c apt-get update     && apt-get install -y --no-install-recommends       "git-all=1:2.7.4-0ubuntu1.6"       "openssh-client=1:7.2p2-4ubuntu2.6"       "screen=4.3.1-2build1"       "sshpass=1.05-1"       "vim=2:7.4.1689-3ubuntu1.2"       "wget=1.17.1-1ubuntu1.4"     && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100

Btw I notice that the code is working with nonexistent data.Am I run in a wrong way?

README for training data?

Hello, could you add a REAME to the data/training data folder with a description of what each file is for?

Could you add the original training data to this directory?

https://github.com/gifford-lab/antibody-2019/tree/master/data/training%20data/Hold%20out%20classification

Also, could you explain why there are "J" in the sequences in the following (and other) file? Are they used as padding tokens for NNs? If so, are paddings added randomly?

https://raw.githubusercontent.com/gifford-lab/antibody-2019/master/data/training%20data/Full%20regression/Lucentis_b/data.tsv

Lastly, could you share the entire phagemid template sequence used? I am interested in looking at the entire antibody sequence available in addition to using the flanking sequence.

Thank you!

gifford-lab / antibody-2019 Goto Github PK

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antibody-2019's Issues

only cdr-h3, where to obtain the full antibody sequence?

Something wrong with Dockerfile building.

README for training data?

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