Sorter does not use custom temporary directory

[GoogleCodeExporter]

there's another problem happening later on in the execution of 
Flux-Capacitor-1.0-SNAPSHOT, it happens right after the "checking" last line of 
stderr below:

######################### begin stderr

[INFO] I am the Flux Toolbox ( Devel Mode ), nice to meet you!

[PRE-CHECK] I am checking availability of the required lpsolve JNI libs.
[PRE-CHECK]     * successfully loaded lpsolve JNI (version 5.5,release 0,build 
14)

*[WARN] Unsorted in line 5 - chr/strand chr1 - already read.
        sorting GTF file  OK (00:00:26)
        scanning [WARN] skipped line chr1       Cufflinks       transcript      234039  236481  1000.0  +       .       transcript_id "CUFF.67.1"; conf_hi "0.000000"; conf_lo "0.000000"; cov "0.673033"; gene_id "CUFF.67"; FPKM "1.0000000000"; frac "0.000000";
 OK (00:00:10)
[WARN] Skipped 155814 lines.
[INFO]  63857 loci, 91971 transcripts, 133381 exons.
                inflating ********** OK (00:16:51)
        checking ********** OK (00:04:40)
########################## end stderr

At this point, flux starts outputting zillions of e.g. 
"sort177509777219203636.srt" files (933KB each) into the /tmp/ directory (even 
though i set 
TMP_DIR to /users/rg/jlagarde/temp/flux/, and even $TMPDIR's "sort" environment 
variable to /home/jlagarde/).

Original issue reported on code.google.com by gmicha@gmail.com on 30 Sep 2011 at 10:47

[GoogleCodeExporter]

sorter ignores user temporary directory

Original comment by gmicha@gmail.com on 30 Sep 2011 at 12:46

• Changed state: Accepted

[GoogleCodeExporter]

Original comment by gmicha@gmail.com on 30 Sep 2011 at 12:46

• Changed state: Fixed