http://updates.iontorrent.com website issue

[kevinzhaok]

It seems the following page is inaccessible. (http://updates.iontorrent.com/tvc_standalone/README.txt).

I also tried to build the TS/tvc docker and found that we can't download packages from http://updates.iontorrent.com
And got the following error:
Connecting to updates.iontorrent.com (updates.iontorrent.com)|12.27.71.44|:80... failed: No route to host.
Is the host down ?

Thanks!

[usasaewan11]

Hi,

I also have same issue and cause module build failed.

How to solve this issue, or any other alternative source to clone these dependency?

Many thanks!

[rfbrondum]

Same problem here, link to the stand alone TVC is dead, and the container to build TS fails when pulling packages.

[sybrohee]

First of all, I am a bit angry at ThermoFisher for completely giving up with the support.

So... after struggling a lot, I found a way to compile tvc and tvcutils (I did not try the other tools as they were less relevant for me).

This is my dockerfile. The idea is to transform the file CMakeLists.dependencies.txt, changing the URL of updates.iontorrent.com which does not exist anymore.

I attach the file tsvc5186files.tar.gz which is copied in the docker file, it contains the correct version of bamtools and the corrected version of CMakeLists.dependencies.txt. It also contains some of the pyhon2 scripts used to run the calling pipeline

tsvc5186files.tar.gz

FROM ubuntu:16.04
RUN apt update
RUN apt install -y wget git zip make cmake build-essential python lsb-release
RUN     apt-get install -y \
        build-essential \
        git-core \
        cmake \
        liblapack-dev \
        libblas-dev \
        libatlas-base-dev \
        gfortran \
        zlib1g-dev \
        libbz2-dev \
        libcurl4-openssl-dev \
        libncurses5-dev \
        libboost-serialization-dev \
        libhdf5-dev \
        python-dev \
        libboost-python-dev \
        python-numpy \
        r-base \
        nano

RUN wget https://codeload.github.com/iontorrent/TS/zip/5fe78dc2f22873845dbbecc7fc2ac8fc33ca42fb -O tsvc_git5fe78dc.zip
RUN unzip tsvc_git5fe78dc.zip
RUN mv TS-5fe78dc2f22873845dbbecc7fc2ac8fc33ca42fb TSVC_5.18.6


RUN mkdir /scripts
COPY src/tsvc5186files.tar.gz /scripts
WORKDIR /scripts
RUN tar xvzf tsvc5186files.tar.gz
RUN mv CMakeLists.dependencies.txt /TSVC_5.18.6/buildTools/cmake/CMakeLists.dependencies.txt

COPY src/bamtools-2.4.0.20150702+git15eadb925f.tar.gz  /TSVC_5.18.6/external

RUN mkdir -p /TSVC_5.18.6/build

WORKDIR /TSVC_5.18.6/build

RUN cmake /TSVC_5.18.6/Analysis/
RUN cmake --build . --target tvc
RUN cmake --build . --target tvcutils

RUN apt install -y samtools

Once it is compiled, you should be able to run tvc using the following command :

docker run dockerimage:tag python2 /scripts/variant_caller_pipeline.py   --input-bam  mybam.bam   --reference-fasta myref.fna             -b targets.bed -N nbcores -B /TSVC_5.18.6/build