install from commandline without GUI possible?

Jalview Discussion
1

Hi,

I tried to install jalview to a specific directory in a commandline-only setup doing the following:

···

#############
wget http://www.jalview.org/old/v2_10_2b1/Web_Installers/InstData/Java/install-jalview.jar

java -jar install-jalview.jar -DUSER_INSTALL_DIR="/tmp/jalview/" -i console
#############

and I get the following error message:

=======================================================

Installer User Interface Mode Not Supported

The installer cannot run in this UI mode. To specify the interface mode, use the -i command-line option, followed by the UI mode identifier. The valid UI modes identifiers are GUI, Console, and Silent.

=======================================================

please note that I did specify the '-i console' flag. Changing to uppercase 'Console' doesnt change anything.. same without any further arguments.

the used setup:
#############
> java -version
openjdk version "1.8.0_144"
OpenJDK Runtime Environment (Zulu 8.23.0.3-linux64) (build 1.8.0_144-b01)
OpenJDK 64-Bit Server VM (Zulu 8.23.0.3-linux64) (build 25.144-b01, mixed mode)
#############

Is there any chance to get that running?

########## Alternatively ##########

is the installation needed at all? What I want to do is to use the jalview commandline interface only..

>>> is this possible using the install-jalview.jar file directly? <<<

Thanks for help,
Martin

--
Dr. Martin Raden, nee Mann, Postdoc

Bioinformatics - Prof. Dr. R. Backofen
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de

2

Hi Jim,

as far as I get it from here:

   https://bioconda.github.io/guidelines.html#java

you have to copy/install all tool-specific files to a tool-version-build-specific folder, ie.

   $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM

thus I guess all dependencies have to go there too.

so maybe building from source is the way to go. I will have a look.

Best,
Martin

···

Am 03.11.2017 um 15:07 schrieb Jim Procter:

Hi Martin - this is a limitation of the installer system we use. The
simplest route may be to compile and put artefacts in place by hand. How
are JVM dependencies handled in conda ?

On 03/11/2017 12:44, Martin Raden wrote:

I tried to install jalview to a specific directory in a commandline-only
setup doing the following:

#############
wget
http://www.jalview.org/old/v2_10_2b1/Web_Installers/InstData/Java/install-jalview.jar

java -jar install-jalview.jar -DUSER_INSTALL_DIR="/tmp/jalview/" -i console
#############

and I get the following error message:

=======================================================

Installer User Interface Mode Not Supported

The installer cannot run in this UI mode. To specify the interface mode,
use the -i command-line option, followed by the UI mode identifier. The
valid UI modes identifiers are GUI, Console, and Silent.

=======================================================

please note that I did specify the '-i console' flag. Changing to
uppercase 'Console' doesnt change anything.. same without any further
arguments.

the used setup:
#############
> java -version
openjdk version "1.8.0_144"
OpenJDK Runtime Environment (Zulu 8.23.0.3-linux64) (build 1.8.0_144-b01)
OpenJDK 64-Bit Server VM (Zulu 8.23.0.3-linux64) (build 25.144-b01,
mixed mode)
#############

Is there any chance to get that running?

########## Alternatively ##########

is the installation needed at all? What I want to do is to use the
jalview commandline interface only..

>>> is this possible using the install-jalview.jar file directly? <<<

Thanks for help,
Martin

--
Dr. Martin Raden, nee Mann, Postdoc

Bioinformatics - Prof. Dr. R. Backofen
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de