[Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages

[Tony Travis]

On 27/05/16 14:54, Geert wrote:
> [...]
> wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo
> sh  
> 
> the error message returns is if nothing happened. 
> 
> Afterwards apt-get update wont work either anymore(same error message).
> 
> I get the feeling the upgrade8.sh script keeps replacing the files that
> I need to change in order to get the thing going.

Hi, Geert.

You're right that is what is happening, but I thought Tim had fixed the
script. Here's a work-around to fix the problem while I check what Tim did:

> Work-around for bug in Google Chrome repo
> 
> # create a work folder
> ajt at beluga:~$ 
> mkdir -p src/bioinformatics/Bio-Linux/xtr
> 
> # create a utility script to capture the upgrade scripts
> cat > get-upgrade8.sh <<EOF
> #!/bin/bash
> #@(#)get-upgrade8.sh  2014-06-30  A.J.Travis
> 
> #
> # Wrapper script for downloading Bio-Linux 8 upgrade
> #
> 
> export UNPACK_ONLY=1
> 
> wget http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> chmod +x upgrade8.sh
> ./upgrade8.sh
> 
> EOF
> 
> # capture the upgrade scripts
> chmod +x get-upgrade8.sh
> ./get-upgrade8.sh |& tee ./get-upgrade8.log
> --2016-05-27 15:53:34--  http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> Resolving nebc.nerc.ac.uk (nebc.nerc.ac.uk)... 192.171.199.66
> Connecting to nebc.nerc.ac.uk (nebc.nerc.ac.uk)|192.171.199.66|:80... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 40029 (39K) [text/x-sh]
> Saving to: ‘upgrade8.sh’
> 
>      0K .......... .......... .......... .........            100% 7.87M=0.005s
> 
> 2016-05-27 15:53:34 (7.87 MB/s) - ‘upgrade8.sh’ saved [40029/40029]
> 
> Working in /tmp/tmp.WL6d9WGD2q...
> x - created lock directory _sh09863.
> x - extracting bio-linux-keyring.deb gzipped
> gunzipping file bio-linux-keyring.deb
> x - extracting pick_cran_mirror.py gzipped
> gunzipping file pick_cran_mirror.py
> x - extracting sources.list.clean gzipped
> gunzipping file sources.list.clean
> x - extracting bl_install_master_list.sh gzipped
> gunzipping file bl_install_master_list.sh
> x - extracting upgrade_to_8.sh gzipped
> gunzipping file upgrade_to_8.sh
> x - extracting pseudo_orphans.txt gzipped
> gunzipping file pseudo_orphans.txt
> x - extracting bl_master_package_list.txt gzipped
> gunzipping file bl_master_package_list.txt
> x - extracting message1.txt gzipped
> gunzipping file message1.txt
> x - removed lock directory _sh09863.
> Unpack complete in /tmp/tmp.WL6d9WGD2q. Exiting.
> 
> # change to the temp directory (/tmp/tmp.WL6d9WGD2q in this case)
> cd /tmp/tmp.WL6d9WGD2q
> 
> # fix the problem repo
> cp -ai upgrade_to_8.sh upgrade_to_8.sh.orig
> vim upgrade_to_8.sh
> ...
> deb [arch=amd64] 
> http://dl.google.com/linux/chrome/deb/ stable main
> ...
> 
> # check the edit
> diff -Naur upgrade_to_8.sh.orig upgrade_to_8.sh
> --- upgrade_to_8.sh.orig	2016-05-27 16:03:19.449332248 +0100
> +++ upgrade_to_8.sh	2016-05-27 16:05:24.475843337 +0100
> @@ -208,7 +208,7 @@
>  cat >/etc/apt/sources.list.d/google-chrome.list <<"."
>  ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
>  # You may comment out this entry, but any other modifications may be lost.
> -deb http://dl.google.com/linux/chrome/deb/ stable main
> +deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main
>  .
>  cat >/etc/apt/sources.list.d/google-talkplugin.list <<"."
>  ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
> 
> 
> # start the upgrade manually
> ./upgrade_to_8.sh

HTH,

  Tony.

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