[ensembl-dev] Release 81 installation problems

[Will McLaren]

Hi all,

This is just a warning, not an error (note it says - "OK!" and "All done").

The warning should be fixed now if you re-download the ensembl-tools
package.

Will McLaren
Ensembl Variation

On 22 July 2015 at 19:31, Balanis, Nikolas G. <NBalanis at mednet.ucla.edu>
wrote:

>  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_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$ ls
> 81_GRCh37  81_GRCh38
> 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_*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> 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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