[ensembl-dev] Release 81 installation problems

Wed Jul 22 19:31:13 BST 2015

Hello Cyriac and other members,

So there was a mistake in what I emailed, It’s not in fact what I ran.

I did run it with the  ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_<http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_>81_GRCh{37,38}.tar.gz $VEP_DATA  instructions. In fact the error message references version 80.

which is the previous version I had installed and used successfully. I have been trying to install version 81  just because I wanted to update to the newest version.

Here is my .vep folder

~/.vep$ ls
homo_sapiens  homo_sapiens_vep_81_GRCh37.tar.gz  homo_sapiens_vep_81_GRCh38.tar.gz

cd homo_sapiens
niko at niko-VirtualBox:~/.vep/homo_sapiens$<mailto:niko at niko-VirtualBox:~/.vep/homo_sapiens$> ls
81_GRCh37  81_GRCh38
niko at niko-VirtualBox:~/.vep/homo_sapiens$<mailto:niko at niko-VirtualBox:~/.vep/homo_sapiens$>

Is there something else I am missing? It seems to me the error is only on version 38. In fact when i run these commands to update GRCh37 I still get the error about 38. If there any other information that would be useful?

niko at niko-VirtualBox:~/vep$ perl INSTALL.pl --AUTO a --SPECIES homo_sapiens --ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
Using non-default installation directory /home/niko/vep - you will probably need to add /home/niko/vep to your PERL5LIB

Setting up directories

Downloading required files
 - fetching ensembl
** GET https://github.com/Ensembl/ensembl/archive/release/81.zip ==> 302 Found (1s)
** GET https://codeload.github.com/Ensembl/ensembl/zip/release/81 ==> 200 OK (42s)
 - unpacking /home/niko/vep/Bio/tmp/ensembl.zip
 - moving files
 - fetching ensembl-variation
** GET https://github.com/Ensembl/ensembl-variation/archive/release/81.zip ==> 302 Found (1s)
** GET https://codeload.github.com/Ensembl/ensembl-variation/zip/release/81 ==> 200 OK (5s)
 - unpacking /home/niko/vep/Bio/tmp/ensembl-variation.zip
 - moving files
 - fetching ensembl-funcgen
** GET https://github.com/Ensembl/ensembl-funcgen/archive/release/81.zip ==> 302 Found
** GET https://codeload.github.com/Ensembl/ensembl-funcgen/zip/release/81 ==> 200 OK (2s)
 - unpacking /home/niko/vep/Bio/tmp/ensembl-funcgen.zip
 - moving files
 - fetching BioPerl
** GET https://github.com/bioperl/bioperl-live/archive/release-1-6-924.zip ==> 302 Found
** GET https://codeload.github.com/bioperl/bioperl-live/zip/release-1-6-924 ==> 200 OK (2s)
 - unpacking /home/niko/vep/Bio/tmp/release-1-6-924.zip
 - moving files

Testing VEP script
./t/filter_vep.t ................ ok
./t/convert_cache.t ............. ok
./t/variant_effect_predictor.t .. 81/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 88/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 89/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 90/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 91/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 92/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 93/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 94/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_otherfeatures_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. 95/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
./t/variant_effect_predictor.t .. ok
All tests successful.
Files=3, Tests=126, 540 wallclock secs ( 0.02 usr  0.03 sys + 20.52 cusr  4.91 csys = 25.48 CPU)
Result: PASS
 - OK!

All done

I get the same error If I try installing version 38. Im not sure why it errors out in that case either as wouldn't I be updating the database to version 81.
 My wild guess is this has something to do with the fasta version 81 of grch38? Any clues? Is there any other information that would be useful?

Thank you so much for your help.

-Nikolas Balanis

Also note that these instructions are just for installing VEP locally to run offline. You won't install all of Ensembl's API and tools.

yes for now I am only using vep. -niko

Hi Nikolas,

The only fix in those commands is to download the v81 cache instead of v79. See the highlighted fix below...

rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_<http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_>81_GRCh{37,38}.tar.gz $VEP_DATA

Also note that these instructions are just for installing VEP locally to run offline. You won't install all of Ensembl's API and tools.

~Cyriac

On Mon, Jul 20, 2015 at 9:58 PM, Balanis, Nikolas G. <NBalanis at mednet.ucla.edu<mailto:NBalanis at mednet.ucla.edu>> wrote:
Hello I am looking for the solution to this problem. I googled and looked on throught the archives but I am not sure how to fix this. I am installing vep based on the instructions from https://github.com/ckandoth/vcf2maf

export VEP_PATH=~/vep

export VEP_DATA=~/.vep

mkdir $VEP_PATH; cd $VEP_PATH

curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/81.tar.gz

tar -zxf 81.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'

rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_79_GRCh{37,38}.tar.gz<http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_79_GRCh%7B37,38%7D.tar.gz> $VEP_DATA

cat $VEP_DATA/*.tar.gz | tar -izxf - -C $VEP_DATA

cd $VEP_PATH

perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA

perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA

I get this warning message below when I perform either of the last 2 instructions.  I can't
seem to figure this out. Everything should be release 81 so I am quite confused.
What are the steps to fix this?
For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.

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