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PSI-Sigma
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Can't locate PDL/GSL/CDF.pm #9

Closed OlgaVT closed 4 years ago

OlgaVT commented 4 years ago

Hi,

I am sorry - it might be mostly the Perl question, but I do not know, how to solve it. When I am using the command: perl ../dummyai.pl --gtf Homo_sapiens.GRCh38.98.sorted.gtf --name PSISigma --type 2 -nread 10

there is an error:

===Intron-read file spent 0.0000 hours.=== Ready to do PSI analysis... Can't locate PDL/GSL/CDF.pm in @INC (you may need to install the PDL::GSL::CDF module) (@INC contains: /nfs/home/users/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /nfs/home/users/perl5/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at (eval 1) line 666. BEGIN failed--compilation aborted at (eval 1) line 666.

I tried:

cpanm PDL::GSL::CDF

The installation was successful. But it did not help. It seems I do not see something obvious. Any help will be appreciated. Thank you!

wososa commented 4 years ago

Did you install GSL like this:

‘ # 2. Install GSL (Using GSL version 2.4 as an example) wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.4.tar.gz tar zxvf gsl-2.4.tar.gz cd gsl-2.4 ./configure make make install cd ..’

OlgaVT commented 4 years ago

Hi, yes, I installed GSL this way also. I do not have root rights, so I did it with ./configure --prefix=/local/folder. Then I added the bin folder to the $PATH and the lib folder to $PERL5LIB and $LD_LIBRARY_PATH, but it did not help. Maybe something wrong with the version of the module, I installed? When I once again tried cpanm PDL::GSL::CDF: --> Working on PDL::GSL::CDF Fetching http://www.cpan.org/authors/id/E/ET/ETJ/PDL-Stats-0.75.tar.gz ... OK Configuring PDL-Stats-0.75 ... OK Building and testing PDL-Stats-0.75 ... OK Successfully installed PDL-Stats-0.75 1 distribution installed

wososa commented 4 years ago

Hi @OlgaVT , Please try echo $PERL5LIB and put the address in $PERL5LIB to the prefix for "/.configure". For example:

echo $PERL5LIB
/home/username/perl5/lib/perl5
./configure --prefix=/home/username/perl5/lib/perl5

Then, run all the steps:

cpan App::cpanminus
cpanm PDL::LiteF
cpanm PDL::Stats

wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.4.tar.gz
tar zxvf gsl-2.4.tar.gz
cd gsl-2.4
./configure
make
make install
cd ..

cpanm PDL::GSL::CDF
cpanm Statistics::Multtest

Hope this helps. Woody

OlgaVT commented 4 years ago

Hi, it helped! Thank you. In the gsl-2.4 folder I did
./configure --prefix=/home/username/perl5/lib/perl5 make make install And it worked. Thank you again!

pre-mRNA commented 3 years ago

Also having this issue. I followed the aforementioned step and GSL is installed properly but cannot be accessed by PSI-Sugma...

pre-mRNA commented 3 years ago

Managed to fix it. Here are the exact steps I used to run PSI-Sugma on the cluster without root permission:

intstall GSL and CDF

echo $PERL5LIB

go to install directory for gsl

cd $dir wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.4.tar.gz tar zxvf gsl-2.4.tar.gz cd gsl-2.4 ./configure --prefix=/path/to/perl5lib make make install cd ..

install perl modules

cpanm PDL::GSL::CDF --reinstall --force --verbose cpanm PDL::GSL::CDF --reinstall --force --verbose cpanm Statistics::Multtest --reinstall --force --verbose cpanm PDL::Stats --reinstall --force --verbose

Thanks woody

wososa commented 3 years ago

@pre-mRNA Thanks for sharing the steps. I fixed this in the dockerfile but didn’t update the page. I will update this.

pre-mRNA commented 3 years ago

Thanks woody.

I am wondering if PSI-Sigma provides PSI-values for all exons transcriptome wide, even those not differentially spliced? I would like to use these data for my own analysis.

Thanks

wososa commented 3 years ago

@pre-mRNA ,

Interesting question. PSI-Sigma doesn't have this function at the moment. One solution is to create a .gtf file pretending all the exons are alternative exons.

Woody

amberdeja commented 1 year ago

Hello,

I have followed all the examples here to install perl dependencies and I keep getting the same error message every time I try to run any of these lines. I hope I can get some help with this.

Thank you, Alejandra

cpanm PDL::LiteF cpanm PDL::GSL::CDF cpanm PDL::Stats

! Installing Capture::Tiny failed. See /c4/home/amartinez/.cpanm/work/1686284776.1884/build.log for details. Retry with --force to force install it. ! Installing the dependencies failed: Module 'Capture::Tiny' is not installed ! Bailing out the installation for Devel-CheckLib-1.16. ! Installing the dependencies failed: Module 'Devel::CheckLib' is not installed ! Bailing out the installation for PDL-2.084.

wososa commented 1 year ago

Hi @amberdeja ,

I apologize for these suffering installing the PDL::GSL::CDF module. I am aware of that the module is not easily installed in certain environments. I can offer two solutions. One is that you can use the Docker image, so you don't need to install the module. The second solution is to follow the Dockerfile of PSI-Sigma's Docker image (ubuntu:16.04):

# Install compiler and perl stuff
RUN apt-get install --yes \
 build-essential \
 gcc-multilib \
 apt-utils \
 perl \
 expat \
 libexpat-dev 

# SET PERL5LIB
ENV PERL5LIB="/usr/local/lib/x86_64-linux-gnu/perl/5.22"
# 1. Install cpanm
RUN cpan App::cpanminus

# 2. Install GSL 
#RUN apt-get update && apt-get upgrade -y
RUN apt-get install -y git make g++ gcc python wget libgsl0-dev

# 3. Install PDL::GSL
RUN cpanm PDL::LiteF
RUN cpanm PDL::GSL::CDF
RUN cpanm PDL::Stats
RUN cpanm Statistics::Multtest
RUN cpanm Statistics::R

Best, Woody

amberdeja commented 1 year ago

Hello Woody,

Thank you for your response. I tried following the solution posted here and it did not work either.

I can run

cpan App::cpanminus

App::cpanminus is up to date (1.7046).

but when I try using apt-get, I get an error message:

apt-get: command not found

I also tried your first solution, but using the Docker image is new to me and is not that intuitive to use it.

Thank you, and please let me know if there is another way to install Psi-sigma. My lab has many data sets that would like to use it on and I really hope I can get it to work

Best wishes,

Alejandra

From: Woody Lin @.> Sent: Friday, June 9, 2023 2:45 AM To: wososa/PSI-Sigma @.> Cc: Alejandra Martinez-Berdeja @.>; Mention @.> Subject: Re: [wososa/PSI-Sigma] Can't locate PDL/GSL/CDF.pm (#9)

Hi @amberdejahttps://github.com/amberdeja ,

I apologize for these suffering installing the PDL::GSL::CDF module. I am aware of that the module is not easily installed in certain environments. I can offer two solutions. One is that you can use the Docker image, so you don't need to install the module. The second solution is to follow the Dockerfile of PSI-Sigma's Docker image (ubuntu:16.04):

Install compiler and perl stuff

RUN apt-get install --yes \ build-essential \ gcc-multilib \ apt-utils \ perl \ expat \ libexpat-dev

SET PERL5LIB

ENV PERL5LIB="/usr/local/lib/x86_64-linux-gnu/perl/5.22"

1. Install cpanm

RUN cpan App::cpanminus

2. Install GSL

RUN apt-get update && apt-get upgrade -y

RUN apt-get install -y git make g++ gcc python wget libgsl0-dev

3. Install PDL::GSL

RUN cpanm PDL::LiteF RUN cpanm PDL::GSL::CDF RUN cpanm PDL::Stats RUN cpanm Statistics::Multtest RUN cpanm Statistics::R

Best, Woody

— Reply to this email directly, view it on GitHubhttps://github.com/wososa/PSI-Sigma/issues/9#issuecomment-1584289039, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADE4RBUBREMDV45GHUR45KLXKLWDJANCNFSM4K3HZGEA. You are receiving this because you were mentioned.Message ID: @.***>

wososa commented 1 year ago

Hi @amberdeja ,

If you are using Ubuntu, apt-get should be installed already. Are you using CentOS or other operation system?

Although I paste many lines of installation in my previous message, the only important piece for the PDL::GSL::CDF module is installing the GSL library.

If you were using CentOS, you can try this command:

#Update yum database with yum using the following command.
sudo yum makecache
#Install gsl-devel using yum by running the following command:
sudo yum -y install gsl-devel

If you are using other operation system, I can try to give other suggestions. So far, I have successfully installed the PDL::GSL::CDF module in Ubuntu, RedHat, CentOS, and MacOS.

If none of these works, I can show you how to use Docker. It is supposed to be much easier. I agree with you, simplicity is the best. Let's try if you can install GSL first.

Best, Woody

amberdeja commented 1 year ago

Hello Woody,

I have macOS Monterey v12.6 installed on my mac.

Thank you, Alejandra

From: Woody Lin @.> Sent: Friday, June 9, 2023 4:14 PM To: wososa/PSI-Sigma @.> Cc: Alejandra Martinez-Berdeja @.>; Mention @.> Subject: Re: [wososa/PSI-Sigma] Can't locate PDL/GSL/CDF.pm (#9)

Hi @amberdejahttps://github.com/amberdeja ,

If you are using Ubuntu, apt-get should be installed already. Are you using CentOS or other operation system?

Best, Woody

— Reply to this email directly, view it on GitHubhttps://github.com/wososa/PSI-Sigma/issues/9#issuecomment-1585231384, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADE4RBX6ZJ2D4A723MA7PV3XKOU7DANCNFSM4K3HZGEA. You are receiving this because you were mentioned.Message ID: @.***>

amberdeja commented 1 year ago

Hello, I just checked and the cluster at ucsf has CentOS Thank you, Alejandra

Get Outlook for iOShttps://aka.ms/o0ukef

From: Alejandra Martinez-Berdeja @.> Sent: Friday, June 9, 2023 6:21:24 PM To: wososa/PSI-Sigma @.> Subject: Re: [wososa/PSI-Sigma] Can't locate PDL/GSL/CDF.pm (#9)

Hello Woody,

I have macOS Monterey v12.6 installed on my mac.

Thank you, Alejandra

From: Woody Lin @.> Sent: Friday, June 9, 2023 4:14 PM To: wososa/PSI-Sigma @.> Cc: Alejandra Martinez-Berdeja @.>; Mention @.> Subject: Re: [wososa/PSI-Sigma] Can't locate PDL/GSL/CDF.pm (#9)

Hi @amberdejahttps://github.com/amberdeja ,

If you are using Ubuntu, apt-get should be installed already. Are you using CentOS or other operation system?

Best, Woody

— Reply to this email directly, view it on GitHubhttps://github.com/wososa/PSI-Sigma/issues/9#issuecomment-1585231384, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADE4RBX6ZJ2D4A723MA7PV3XKOU7DANCNFSM4K3HZGEA. You are receiving this because you were mentioned.Message ID: @.***>

amberdeja commented 1 year ago

Hello Woody,

Sorry to bother you again, but it is a bit frustrating that I have everything ready to run PSIsigma and I just need those three perl dependencies installed. The rest runs fine.

cpanm PDL::LiteF cpanm PDL::GSL::CDF cpanm PDL::Stats

I am using the C4 cluster at UCSF and it uses centOS. Do you have some other instructions I could use to install perl using anaconda? I would really appreciate if you could help me get it installed because there are multiple data sets that we would like to run with Psi-sigma.

Thank you, Alejandra

From: Woody Lin @.> Sent: Friday, June 9, 2023 4:14 PM To: wososa/PSI-Sigma @.> Cc: Alejandra Martinez-Berdeja @.>; Mention @.> Subject: Re: [wososa/PSI-Sigma] Can't locate PDL/GSL/CDF.pm (#9)

Hi @amberdejahttps://github.com/amberdeja ,

If you are using Ubuntu, apt-get should be installed already. Are you using CentOS or other operation system?

Best, Woody

— Reply to this email directly, view it on GitHubhttps://github.com/wososa/PSI-Sigma/issues/9#issuecomment-1585231384, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADE4RBX6ZJ2D4A723MA7PV3XKOU7DANCNFSM4K3HZGEA. You are receiving this because you were mentioned.Message ID: @.***>

wososa commented 1 year ago

Hi @amberdeja ,

yes, conda will be needed if you use computing cluster. I plan to share my conda environment with you soon. Please send me an email so that easier to communicate.

best, Woody

wososa commented 1 year ago

Hi @mohawk2 ,

If you can comment on the installation of PDL::GSL::CDF on CentOS system, it will be helpful too! :)

Best, Woody

mohawk2 commented 1 year ago

If you can comment on the installation of PDL::GSL::CDF on CentOS system, it will be helpful too! :)

What's going on here is that PDL::GSL::CDF was moved from the PDL::Stats distro to the main PDL distro, to live alongside the rest of the PDL::GSL modules. This took place with PDL::Stats 0.77, and PDL 2.038.

So, if you want to use PDL::GSL::CDF, you need to use either PDL::Stats <0.77, or PDL >= 2.038. I don't know which version of CentOS you have, or which PDL that will have.

wososa commented 1 year ago

@amberdeja ,

mohawk2 is the developer of PDL modules. If you want to try installing PDL::GSL::CDF locally, you can try his comments like this:

cpanm PDL::Stats@0.76
cpanm PDL@2.038
cpanm PDL::GSL::CDF

Best, Woody