VEP

[zehraagha]

I need DBD-MYSQL module to be installed as it is a dependency of a software package I am runnning. Kindly see below the link, which I used to download the DBD-mYSQL. https://metacpan.org/dist/DBD-mysql/view/lib/DBD/mysql/INSTALL.pod When I try to follow installation instructions I get the following error :"error while loading shared libraries: libmysqlclient.so.22: cannot open shared object file: No such file or directory"

Kindly look into this.

[dsajdak]

Hi @zehraagha when I suggested submitting a build request it was for the VEP ensemble software that you said you were attempting to install. This is available in Easybuild and may be of interest to other users at our center. We don't generally install individual dependencies for software, especially database software, like you're requesting here. If you'd like us to install VEP, please let me know.

[zehraagha]

Okay kindly do this for me.

Zehra agha

On Thu, Mar 28, 2024 at 3:45 PM Dori Sajdak @.***> wrote:

Hi @zehraagha https://github.com/zehraagha when I suggested submitting a build request it was for the VEP ensemble software that you said you were attempting to install. This is available in Easybuild and may be of interest to other users at our center. We don't generally install individual dependencies for software, especially database software, like you're requesting here. If you'd like us to install VEP, please let me know.

— Reply to this email directly, view it on GitHub https://github.com/ubccr/software-layer/issues/275#issuecomment-2025983131, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHKGEX2WTVQAC2TEFRPTALLY2RXNDAVCNFSM6AAAAABFNLXYBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRVHE4DGMJTGE . You are receiving this because you were mentioned.Message ID: @.***>

[tonykew]

Note: libmysqlclient.so.22 is available in the mysql/8.2.0-clientonly module e.g.

$ module load gcc/11.2.0 mysql/8.2.0-clientonly
login2$ ls -l ${EBROOTMYSQL}/lib
total 17238
-rw-r--r-- 1 cvmfs cvmfs 9777344 Jan 17 12:52 libmysqlclient.a
lrwxrwxrwx 1 cvmfs cvmfs      20 Jan 17 12:52 libmysqlclient.so -> libmysqlclient.so.22
lrwxrwxrwx 1 cvmfs cvmfs      24 Jan 17 12:52 libmysqlclient.so.22 -> libmysqlclient.so.22.1.0
-rwxr-xr-x 1 cvmfs cvmfs 7868232 Jan 17 12:52 libmysqlclient.so.22.1.0
drwxr-xr-x 2 cvmfs cvmfs    4096 Jan 17 13:56 pkgconfig
$ 

Though this may also be part of the DBD-mysql module build.

I will work on building VEP, but there are a great many dependent modules I will have to build first, so this will likely take some time.

[zehraagha]

Awesome, thanks for the info! I will keep waiting

On Wed, Apr 3, 2024 at 10:53 AM Tony Kew @.***> wrote:

Note: libmysqlclient.so.22 is available in the mysql/8.2.0-clientonly module e.g.

$ module load gcc/11.2.0 mysql/8.2.0-clientonly login2$ ls -l ${EBROOTMYSQL}/lib total 17238 -rw-r--r-- 1 cvmfs cvmfs 9777344 Jan 17 12:52 libmysqlclient.a lrwxrwxrwx 1 cvmfs cvmfs 20 Jan 17 12:52 libmysqlclient.so -> libmysqlclient.so.22 lrwxrwxrwx 1 cvmfs cvmfs 24 Jan 17 12:52 libmysqlclient.so.22 -> libmysqlclient.so.22.1.0 -rwxr-xr-x 1 cvmfs cvmfs 7868232 Jan 17 12:52 libmysqlclient.so.22.1.0 drwxr-xr-x 2 cvmfs cvmfs 4096 Jan 17 13:56 pkgconfig $

Though this may also be part of the DBD-mysql module build.

I will work on building VEP, but there are a great many dependent modules I will have to build first, so this will likely take some time.

— Reply to this email directly, view it on GitHub https://github.com/ubccr/software-layer/issues/275#issuecomment-2034843366, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHKGEX6JZ3SJCBAN5WSJQG3Y3QJXDAVCNFSM6AAAAABFNLXYBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZUHA2DGMZWGY . You are receiving this because you were mentioned.Message ID: @.***>

-- Regards

Dr. Zehra Agha Research Scientist SUNY at University at Buffalo Phone#(435)215-9997 @.*** 8031, Buffalo medical centre Buffalo, NY

[tonykew]

I have completed a test build of VEP version 105 - more info to follow

[zehraagha]

Thankyou so much. can I try it with the interactive session on ccr?

On Wed, Apr 3, 2024 at 12:03 PM Tony Kew @.***> wrote:

I have completed a test build of VEP version 105 - more info to follow

— Reply to this email directly, view it on GitHub https://github.com/ubccr/software-layer/issues/275#issuecomment-2035008253, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHKGEXYR7LXMH7CFHDIB72DY3QR35AVCNFSM6AAAAABFNLXYBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZVGAYDQMRVGM . You are receiving this because you were mentioned.Message ID: @.***>

-- Regards

Dr. Zehra Agha Research Scientist SUNY at University at Buffalo Phone#(435)215-9997 @.*** 8031, Buffalo medical centre Buffalo, NY

[tonykew]

Thank you so much. Can I try it with the interactive session on ccr?

Not yet - we have to go through an internal testing process before the software is published to the ccrsoft/2023.01 software release

[zehraagha]

Dear Tony

I am concerned about one thing. As I can see you are building VEP version 105 although version 111 is the latest version.

On Wed, Apr 3, 2024 at 1:14 PM Tony Kew @.***> wrote:

Thank you so much. Can I try it with the interactive session on ccr?

Not yet - we have to go through an internal testing process before the software is published to the ccrsoft/2023.01 software release

— Reply to this email directly, view it on GitHub https://github.com/ubccr/software-layer/issues/275#issuecomment-2035148047, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHKGEXZT76ZUOJXFTEGUFLLY3Q2HFAVCNFSM6AAAAABFNLXYBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZVGE2DQMBUG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Regards

Dr. Zehra Agha Research Scientist SUNY at University at Buffalo Phone#(435)215-9997 @.*** 8031, Buffalo medical centre Buffalo, NY

[tonykew]

I built the version that is supported by the current easyconfigs for our supported toolchains: https://docs.ccr.buffalo.edu/en/latest/software/releases/#202301 specifically, GCC version 11.2.0

VEP version 105 has been published to the ccrsoft/2023.01 software release:

$ module spider vep
----------------------------------------------------------------------------
  vep: vep/105
----------------------------------------------------------------------------
    Description:
      Variant Effect Predictor (VEP) determines the effect of your variants
      (SNPs, insertions, deletions, CNVs or structural variants) on genes,
      transcripts, and protein sequence, as well as regulatory regions.
      Includes EnsEMBL-XS, which provides pre-compiled replacements for
      frequently used routines in VEP.

    You will need to load all module(s) on any one of the lines below before the "vep/105" module is available to load.

      gcc/11.2.0
[...]
$ module load gcc/11.2.0 vep/105
$ 

This module includes several binaries:

$ ls -l ${EBROOTVEP} | grep ^-r.x
-rwxr-xr-x 1 cvmfs cvmfs 16698 Dec  7  2021 convert_cache.pl
-rwxr-xr-x 1 cvmfs cvmfs 16620 Dec  7  2021 filter_vep
-rwxr-xr-x 1 cvmfs cvmfs  4880 Dec  7  2021 haplo
-rwxr-xr-x 1 cvmfs cvmfs 56613 Apr  3 11:28 INSTALL.pl
-rwxr-xr-x 1 cvmfs cvmfs 56607 Dec  7  2021 INSTALL.pl.orig.eb
-rwxr-xr-x 1 cvmfs cvmfs  5246 Dec  7  2021 variant_recoder
-rwxr-xr-x 1 cvmfs cvmfs 14462 Dec  7  2021 vep
$ 

For example:

$ vep --help
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

Versions:
  ensembl              : 105.525fbcb
  ensembl-funcgen      : 105.660df8f
  ensembl-io           : 105.2a0a40c
  ensembl-variation    : 105.ac8178e
  ensembl-vep          : 105.0

Help: dev@ensembl.org , helpdesk@ensembl.org
Twitter: @ensembl

http://www.ensembl.org/info/docs/tools/vep/script/index.html

Usage:
./vep [--cache|--offline|--database] [arguments]
[...]
$ 

Note that you won't be able to upgrade the installed software version with the "INSTALL.pl" script, because our software releases are read only. If you need this capability, you will have to build your own version of VEP (e.g. in a /projects/academic/jbwillia/[...] directory) Since I have built all the dependencies, this process would be something like:

$ ssh compile
$ export CCR_BUILD_PREFIX="/projects/academic/jbwillia/software"
$ export CCR_CUSTOM_BUILD_PATHS="${CCR_BUILD_PREFIX}"
$ module load Easybuild
$ eb VEP-105-GCC-11.2.0.eb
[...]
$ mkdir -p $HOME/.ccr
$ echo $CCR_CUSTOM_BUILD_PATHS >> ~/.ccr/modulepaths
$ 

See the following docs for more info on building your own software: https://docs.ccr.buffalo.edu/en/latest/software/building/