Perl Downloads
Perl Downloads ->>->>->> https://urllie.com/2t7baj
By default the biomart-perl API will be looking at the biomart.org website, this can be changed in the "biomart-perl/conf/martURLLocation.xml" file. The following URL will give you the Ensembl.org Mart registry information. For example in release 79: Paste the text obtained on the following page into the biomart-perl/conf/martURLLocation.xml file.
Edit the "$action" variable to "clean" as indicated by the 2 in the image below. The variable need to be set up to "clean" everytime the "biomart-perl/conf/martURLLocation.xml" get updated as some data will be cached on your computer.
Once you have run your script once, you can update the "$action" variable from "clean" to "cached". The run will be faster and you should get the following output:perl hgnc_swissprot.plProcessing Cached Registry: ../conf/cachedRegistries/martURLLocation.xml.cachedEnsembl Gene ID Ensembl Transcript ID HGNC symbol UniProt/SwissProt AccessionENSG00000139618 ENST00000380152 BRCA2 P51587ENSG00000139618 ENST00000528762 BRCA2ENSG00000139618 ENST00000470094 BRCA2ENSG00000139618 ENST00000544455 BRCA2 P51587 Ensembl release 109 - Feb 2023 © EMBL-EBI EMBL-EBI
Normally if you want to install a Perl module from CPAN you don't needto manually download it, as there are clients for CPAN that will do it for you.However when I research a module, for example to write an article about it, or to see how another module is using it, I often prefer to havethe whole distribution on my disk. That way I have the tests included with the distribution and, and if it contains examplesI have those too. Let's say I'd like to download the distribution that contains the WWW::Mechanize module.cpanmIf you have CPAN Minus installed you can type in cpanm --look WWW::Mechanize. It will download the distribution,unzip it and open a subshell in the unzipped directory. That's cool, but in many cases I'd need to have several distributions to be around, andI don't really like that subshell. I'd like the downloaded and unzipped directory to be easily accessible later on from my regular shell.cpanAs pointed out by dnmfarrell on Reddit,the cpan command, which is the regular cpan client also has a usefule option.cpan -g WWW::Mechanize would download the zip file of the latest distribution providing the WWW::Mechanize module andwould save it in the current directory. I would still need to unzip it, but this is also a great solution.There might be some bug using this feature on a newly configured cpan client as I've reported here,but I think if you regularily use this cpan client then it will work fine.git-cpanThen there is the git-cpan command line toolthat comes with Git::CPAN::Patch.It seems to be everything I could want and more. It would fetch a distribution from CPAN, create a local Git repositoryand let you hack on the code.I tried git-cpan clone WWW::Mechanize. It recognized that WWW::Mechanize already has a repository on GitHub,and cloned that repository. Unfortunately when I tried to run git-cpan clone XML::DT (a module that does notdeclare its repository), I got several errors. I have reported the issue.Using WWW::MechanizeMy main issue though is that I wanted something simple. So here is what I wrote:examples/download-cpan.pl#!/usr/bin/env perluse strict;use warnings;use 5.010;use WWW::Mechanize;my $dir = '/tmp';my $url = shift or die "Usage: $0 URL\n";my $name;if ($url =~ m{^ ([a-zA-Z0-9:]+)$}) {$name = $1;} elsif ($url =~ m{^ ([a-zA-Z0-9-]+)$}) {$name = $1;}die "Invalid URL\n" if not $name;my $w = WWW::Mechanize->new;$w->get($url);my $download_link = $w->find_link( text_regex => qr{^Download} );die "Could not find download link\n" if not $download_link;say $download_link;exit;my ($file) = $download_link->url =~ m{([^/]+)$};say $download_link->url;say $file;my $path = "$dir/$file";if (-e $path) {say "Already downloaded to $path";exit;}$w->follow_link( text_regex => qr{^Download} );$w->save_content( $path, binary => 1 );say "Saved to $path";chdir $dir;system "tar xzf $file";A very simple and probably fragile solution.The script accepts a URL on the command line. One that either leads to a module on MetaCPAN, such as this: ::Mechanize or one that leads to a distribution. Such as this: -Mechanize.It looks for the link that says Download ..., take the URL where that link leads. Downloads the thing behind the link,saves it to the /tmp directory an unzips it.The script uses WWW::Mechanize module to fetch the HTML page of MetaCPANGet the parameter from the command line. Exit with an error message if there was not parameter on the command line.:my $url = shift or die "Usage: $0 URL\n";Check if the given parameter is in the format of either of the pages mentioned above and extract the name of themodule or distribution into the $name variable. Both regexes start by matching a URL on the MetaCPANsite and then containing letters, numbers and some extra characters.my $name;if ($url =~ m{^ ([a-zA-Z0-9:]+)$}) { $name = $1;} elsif ($url =~ m{^ ([a-zA-Z0-9-]+)$}) { $name = $1;}If $name is empty, exit the script with an error message. This was not one of the recognized URL formats:die "Invalid URL\n" if not $name;Create the WWW::Mechanzie object and fetch the URL the user gave us:my $w = WWW::Mechanize->new;$w->get($url);On the downloaded page try to find a link that matches the regex ^Download. That is a link that starts with the word DownloadExit the script with an error message if no such link could be found:my $download_link = $w->find_link( text_regex => qr{^Download} );die "Could not find download link\n" if not $download_link;The value returned by the find_link method is either undef, if no link was found,or an instance of WWW::Mechanize::Link.From the object we can extract the URL of the link using the url method and then using a regular expression we extractthe last part of the string. The regex itself will match [^/] (any character except slash, till the end of the string.That is it will match the name of the file at the end of the URL:my ($file) = $download_link->url =~ m{([^/]+)$};say $download_link->url;say $file;From the filename and from the $dir variable we declared at the beginning of the script we create a local pathwhere we would like to save the downloaded zip file. We check if the file already exists and exit the script if the file is there.Apparently we have already downloaded this version of this distribution:my $path = "$dir/$file";if (-e $path) { say "Already downloaded to $path"; exit;}The follow_link method will search for the link again and click on it. Effectively downloading the content of the filebut keeping it in memory as the content of the page.$w->follow_link( text_regex => qr{^Download} );The save_content method will save the content of the current page which should be the content of the content of the zip file.Still zipped. In the $path variable we provide the local path where the content should be save and we also tell it to save thecontent as a binary file. After all we are talking about a zip file.$w->save_content( $path, binary => 1 );Once that's done, we change to the directory where we saved this file and call the external tar command to unzip the file.chdir $dir;system "tar xzf $file";A rather simple use of the WWW::Mechanize module. Written by Gabor Szabo Published on 2015-03-14
Alternately, if you have Fink installed then you can use it to install the Template Toolkit. Christian Schaffner maintains the Fink packages for the Template Toolkit. They can be found in the libs/perlmods. section.
For some reason the file is not downloading. I have used LWP::Simple before with images and they work just fine. The only difference they have with this is that it is an excel file and also the URL auto downloads the file when you enter the URL.
I have been trying to run a simple perl-cgi script on windows 7. This is a simple HTML form with an OK button where clicking on OK button displays some text. But clicking the OK button on the HTML page, instead of executing and displaying perl file's output, the browser starts downloading the script. I have added handler in httpd.conf
I have tried this on chrome, IE and Mozilla. Mozilla and chrome start the perl file download, but IE just displays some weird content on clicking the OK button. How can I make the browser display output of file execution rather than starting the script download ?
Source archives for all releases of perl5. You should only need to look here if you have an application which, for some reason or another, does not run with the current release of perl5. Be aware that only 5.004 and later versions of perl are maintained. If you report a genuine bug in such a version, you will probably be informed either that it is fixed in the current maintenance release, or will be fixed in a subsequent one. If you report a bug in an unmaintained version, you are likely to be advised to upgrade to a maintained version which fixes the bug, or to await a fix in a maintained version. No fix will be provided for the unmaintained version.
This is where we hid the source for perl4, which was superseded by perl5 years ago. We would really much rather that you didn't use it. It is definitely obsolete and has security and other bugs. And, since it's unsupported, it will continue to have them.
Files relevant to the security problem found in 'suidperl' in August 2000, reported in the bugtraq mailing list. The problem was found in all Perl release branches: 5.6, 5.005, and 5.004. The 5.6.1 release has a fix for this, as have the 5.8 releases. The (now obsolete) development branch 5.7 was unaffected, except for very early (pre-5.7.0) developer-only snapshots. The bug affects you only if you use an executable called 'suidperl', not if you use 'perl', and it is very likely only to affect UNIX platforms, and even more precisely, as of March 2001, the only platforms known to be affected are Linux platforms (all of them, as far as we know). The 'suidperl' is an optional component which is not installed, or even built, by default. These files will help you in the case you compile Perl yourself from the source and you want to close the security hole. 2b1af7f3a8