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 _______________________________________________ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
