Installation problems

[GoogleCodeExporter]

For which program(s) you want a new feature?
(Capacitor)

Which build of the program(s)?

FluxCapacitor-v1.2-j1.5

What operating system you use?
(unix64)
x86_64

What steps will reproduce the problem?
1. gunzipped and untarred the downloded file
2. java -version
gives:

java version "1.5.0_17"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_17-b04)
Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_17-b04, mixed mode)

3. http://flux.sammeth.net/cap_installation.html then says: "run the batch
file". Which batch file? I presume this means the 'installation.sh' script.
4. running the installation.sh script gives:

sh ./install.sh
dirname: extra operand `install.bat'
Try `dirname --help' for more information.
Unable to access jarfile /../lib/FluxCapacitor.jar

It looks like install.sh should be running something like this:

java
-DwrapperDir=/lustre/cbi4/work1/wormpub/gary/Dev/RGASP-Pipeline/FluxCapacitor-v1
.2-j1.5
-jar
"/lustre/cbi4/work1/wormpub/gary/Dev/RGASP-Pipeline/FluxCapacitor-v1.2-j1.5/../l
ib/FluxCapacitor.jar"
--install

but this gives:
Unable to access jarfile
/lustre/cbi4/work1/wormpub/gary/Dev/RGASP-Pipeline/FluxCapacitor-v1.2-j1.5/../li
b/FluxCapacitor.jar

Original issue reported on code.google.com by g...@sanger.ac.uk on 14 Aug 2009 at 12:50

[GoogleCodeExporter]

Downloading the FluxCapacitor version with samples works better.
This now gives:
sh install.sh

[HELLO] I am the FLUX CAPACITOR (v1.2), nice to meet you!

[INSTALL] I am installing the program on your system.
        * base path: ./..

        * found OS=Linux, ARCH=amd64, 64 bit
        * guessed library path
/lustre/cbi4/work1/wormpub/gary/Dev/RGASP-Pipeline/FluxCapacitor-v1.2-j1.5/lib/n
ative/lpsolve55/unix/x86/64

and the bin/flux.sh script is created.

Original comment by g...@sanger.ac.uk on 14 Aug 2009 at 1:10

[GoogleCodeExporter]

Accepted. I have started looking into this issue. The demonstration files (from
january!) are no longer good for the current versions of the Capacitor as they 
have
non-unique read IDs (i.e., "nobody").

I will add a couple of file checks and warnings, and provide a new sample file 
bundle.

Original comment by gmicha@gmail.com on 15 Aug 2009 at 6:00

• Changed state: Accepted
• Added labels: Capacitor

[GoogleCodeExporter]

From Flux Capacitor v1.0 RC1 on, read identifier formats can be defined by a 
flexible expression system.

Original comment by gmicha@gmail.com on 21 Sep 2011 at 10:02

• Changed state: Fixed