Question: I am moving the comment I made here ([whatever not displayed][1]) to a real question:

I am trying to use **backlocate** to get the genomic position (say, on hg19) from a mutation given with the classic nomenclature: p.D240Y (gene EIF4G1).

There are two versions of the tool available:

- one from [github][2]
- one from [google code][3] (from my understanding, this is the one intended for distribution)

I tried cloning the github repository and compiling the 'jsandbox' tools. However, I get a `java.lang.ClassNotFoundException: com.mysql.jdbc.Driver` error that I couldn't get fixed even when installing 'Mysql Connector Driver' and adding it to my `$CLASSPATH`.

After having tried a lot of things, I realized there was a version apparently made for distribution (in the 'variationtoolkit' from google code). I checked-out the complete toolkit, but the compilation fails due to some unmet dependencies that I can't seem to install properly (tabix).

Has anyone had experience using **backlocate**, or would @Pierre have some ideas on how to fix these errors?

[1]: https://www.biostars.org/p/15992/
[2]: https://github.com/lindenb/jsandbox/blob/master/src/sandbox/BackLocate.java
[3]: https://code.google.com/p/variationtoolkit/wiki/BackLocate

Answer: Hi leonor,

As its seems that using the sql driver is a problem for many users, I've just moved my code to only use local resources (https://github.com/lindenb/jvarkit/commit/f8cb884544354a7c62d4440b58e8e74c2045a6cd). You don't need the jdbc driver anymore :

Download a fresh copy of jvarkit and compile again

```
[lindenb@kaamelot-master01 jvarkit-git]$ echo -e "NOTCH2\tP1090M" | java -jar dist/backlocate.jar -R hg19.fasta
[INFO/BackLocate] 2014-11-05 12:11:00 "Starting JOB at Wed Nov 05 12:11:00 CET 2014 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=7ddcffc73f823f9e377ffd2a3644cbf50cf26581 built=2014-11-05 12:02:52"
[INFO/BackLocate] 2014-11-05 12:11:00 "Command Line args : -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37_prefix.fasta"
[INFO/BackLocate] 2014-11-05 12:11:00 "Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-b19"
[WARNING/BackLocate] 2014-11-05 12:11:00 "Undefined knwonGeneURI, using http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz"
[WARNING/BackLocate] 2014-11-05 12:11:00 "Undefined kgXref, using http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz"
[INFO/BackLocate] 2014-11-05 12:11:00 "loading genes"
[WARNING/BackLocate] 2014-11-05 12:11:04 "The reference doesn't contain chromosome chr17_ctg5_hap1"
[WARNING/BackLocate] 2014-11-05 12:11:07 "The reference doesn't contain chromosome chr4_ctg9_hap1"
[WARNING/BackLocate] 2014-11-05 12:11:07 "The reference doesn't contain chromosome chr6_apd_hap1"
[WARNING/BackLocate] 2014-11-05 12:11:07 "The reference doesn't contain chromosome chr6_cox_hap2"
[WARNING/BackLocate] 2014-11-05 12:11:08 "The reference doesn't contain chromosome chr6_dbb_hap3"
[WARNING/BackLocate] 2014-11-05 12:11:08 "The reference doesn't contain chromosome chr6_mann_hap4"
[WARNING/BackLocate] 2014-11-05 12:11:08 "The reference doesn't contain chromosome chr6_mcf_hap5"
[WARNING/BackLocate] 2014-11-05 12:11:08 "The reference doesn't contain chromosome chr6_qbl_hap6"
[WARNING/BackLocate] 2014-11-05 12:11:08 "The reference doesn't contain chromosome chr6_ssto_hap7"
[INFO/BackLocate] 2014-11-05 12:11:10 "genes:78963"
[INFO/BackLocate] 2014-11-05 12:11:10 "loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz"
[INFO/BackLocate] 2014-11-05 12:11:18 "kgxref:28493"
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna codon base.in.rna chromosome index0.in.genomic exon
[INFO/BackLocate] 2014-11-05 12:11:18 "reading from stdin"
[INFO/BackLocate] 2014-11-05 12:11:18 "fetch genome"
##uc001eik.3
NOTCH2 P 1090 M uc001eik.3 - P 3267 CCA C chr1 120480548 Exon 20
NOTCH2 P 1090 M uc001eik.3 - P 3268 CCA C chr1 120480547 Exon 20
NOTCH2 P 1090 M uc001eik.3 - P 3269 CCA A chr1 120480546 Exon 20
##uc001eil.3
NOTCH2 P 1090 M uc001eil.3 - P 3267 CCA C chr1 120480548 Exon 20
NOTCH2 P 1090 M uc001eil.3 - P 3268 CCA C chr1 120480547 Exon 20
NOTCH2 P 1090 M uc001eil.3 - P 3269 CCA A chr1 120480546 Exon 20
#index out of range for :uc001eim.4 petide length=820
#index out of range for :uc021osy.1 petide length=864
[INFO/BackLocate] 2014-11-05 12:11:18 "End JOB status=0 [Wed Nov 05 12:11:18 CET 2014] com.github.lindenb.jvarkit.tools.backlocate.BackLocate done. Elapsed time: 0.31 minutes."
```