[Bioperl-l] problem installing BioPerl
Scott Cain
scott at scottcain.net
Mon Aug 26 18:27:16 UTC 2013
Hi Alexey,
Since I didn't exactly know the answer (I'm not a maintainer), I just
created a new Ubuntu 12.04.3 server and installed it fresh to see what it
would install. The list of both suggested packages (that won't get
installed without an additionally apt-get command) and the list of newly
installed packages are pasted below. It's a long list! The Debian package
installs lots of additional software, most of which the typical user isn't
going to need, but it is easy.
Scott
Suggested packages:
apache2-doc apache2-suexec apache2-suexec-custom filo gmap paml molphy
phylip ensembl
ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 libvibrant6a bowtie-examples
clustalx seaview
emboss-doc emboss-test embassy ghostscript-cups ghostscript-x hpijs
graphviz-doc
fonts-ipafont-mincho fonts-ipafont-gothic ttf-arphic-ukai ttf-arphic-uming
fonts-unfonts-core hmmer-doc libmath-random-perl libxml-sax-expatxs-perl
cups-common
libgd-tools libdata-dump-perl libjasper-runtime liblcms2-utils uuid
ttf-baekmuk
ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp
libscalar-number-perl libmime-lite-perl libnet-jabber-perl
libauthen-ntlm-perl
libunicode-map8-perl libunicode-string-perl xml-twig-tools
libyaml-shell-perl groff
ncbi-epcr probcons-extra ri ruby-dev ruby1.8-examples ri1.8
openssl-blacklist boxshade
t-coffee-doc t-coffee-examples dialign-tx poa proda wise-doc
The following NEW packages will be installed:
amap-align apache2 apache2-mpm-worker apache2-utils apache2.2-bin
apache2.2-common bedtools
bioperl bioperl-run blast2 bowtie bwa clustalw cmap-adobe-japan1 dialign
emboss emboss-data
emboss-lib exonerate fontconfig fontconfig-config fonts-liberation
ghostscript graphviz
gs-cjk-resource gsfonts hmmer infernal kalign libace-perl
libalgorithm-c3-perl
libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl
libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapr1
libaprutil1
libaprutil1-dbd-sqlite3 libaprutil1-ldap libarray-compare-perl
libavahi-client3
libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl
libbio-asn1-entrezgene-perl
libbio-perl-perl libbio-perl-run-perl libbit-vector-perl
libbsd-resource-perl
libcache-cache-perl libcairo2 libcap2 libcarp-clan-perl libcdt4
libcgraph5 libclass-c3-perl
libclass-c3-xs-perl libclass-inspector-perl libclass-load-perl
libclass-load-xs-perl
libclone-perl libconvert-binary-c-perl libconvert-binhex-perl
libcrypt-ssleay-perl libcups2
libcupsimage2 libdata-optlist-perl libdata-stag-perl libdate-calc-perl
libdate-calc-xs-perl
libdate-manip-perl libdatrie1 libdbd-mysql-perl libdbd-pg-perl
libdbd-sqlite3-perl
libdbi-perl libdevel-globaldestruction-perl libdevel-partialdump-perl
libdevel-symdump-perl
libencode-locale-perl liberror-perl libeval-closure-perl libfcgi-perl
libfile-listing-perl
libfont-afm-perl libfontconfig1 libfreezethaw-perl libgd-gd2-perl
libgd2-xpm libgraph-perl
libgraph4 libgraphviz-perl libgs9 libgs9-common libgvc5 libgvpr1
libheap-perl libhpdf-2.2.1
libhtml-form-perl libhtml-format-perl libhtml-parser-perl
libhtml-tagset-perl
libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl
libhttp-date-perl
libhttp-message-perl libhttp-negotiate-perl libice6 libijs-0.35
libio-pty-perl
libio-socket-inet6-perl libio-socket-ssl-perl libio-stringy-perl
libipc-run-perl
libipc-sharelite-perl libjasper1 libjbig2dec0 libjcode-pm-perl
libjpeg-turbo8 libjpeg8
liblcms2-2 liblist-moreutils-perl liblwp-mediatypes-perl
liblwp-protocol-https-perl
libmailtools-perl libmath-derivative-perl libmath-spline-perl
libmime-tools-perl
libmldbm-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl
libmysqlclient18
libnamespace-clean-perl libncbi6 libnet-daemon-perl libnet-http-perl
libnet-ssleay-perl
libole-storage-lite-perl libossp-uuid-perl libossp-uuid16
libpackage-deprecationmanager-perl
libpackage-stash-perl libpackage-stash-xs-perl libpango1.0-0
libpaper-utils libpaper1
libparams-classify-perl libparams-util-perl libparse-recdescent-perl
libpathplan4
libperl5.14 libpixman-1-0 libplrpc-perl libpostscript-perl libpq5
libreadline5 libruby1.8
libset-scalar-perl libsm6 libsoap-lite-perl libsocket6-perl
libsort-naturally-perl
libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl
libstatistics-descriptive-perl
libsub-exporter-perl libsub-identify-perl libsub-install-perl
libsvg-graph-perl libsvg-perl
libtask-weaken-perl libthai-data libthai0 libtie-ixhash-perl libtiff4
libtree-dagnode-perl
libtry-tiny-perl libunicode-map-perl liburi-perl libvariable-magic-perl
libwww-perl
libwww-robotrules-perl libxaw7 libxcb-render0 libxcb-shm0 libxft2
libxml-dom-perl
libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl
libxml-libxslt-perl
libxml-namespacesupport-perl libxml-parser-perl libxml-perl
libxml-regexp-perl
libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl
libxml-sax-writer-perl
libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpath-perl
libxml-xpathengine-perl libxmu6 libxpm4 libxrender1 libxslt1.1 libxt6
libyaml-libyaml-perl
libyaml-perl libyaml-syck-perl lynx lynx-cur mafft maq muscle
mysql-common ncbi-data
perl-doc perl-tk phyml primer3 probcons ruby ruby1.8 samtools sim4
ssl-cert t-coffee
tigr-glimmer ttf-dejavu-core ttf-liberation wise x11-common
0 upgraded, 239 newly installed, 0 to remove and 0 not upgraded.
Need to get 94.7 MB of archives.
After this operation, 271 MB of additional disk space will be used.
On Sun, Aug 25, 2013 at 10:45 PM, Keith Keller <
kkeller at wombat.san-francisco.ca.us> wrote:
> On 2013-08-26, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:
> > By the way, would you please explain what's the difference (if any)
> between
> > installing bioperl via CPAN, by 'sudo apt-get install libbio-perl-perl'
> and
> > just 'sudo apt-get install bioperl'.
>
> Installing from CPAN installs what the Bioperl authors distribute.
> Installing via apt-get installs what the distribution maintainers
> redistribute. You'd have to ask the distro maintainers what the
> difference between the two packages are (if any; it's possible one is an
> alias for the other).
>
> > It seems like CPAN install does not
> > carry along the external software dependencies (eg clustalw), but I'm not
> > sure.
>
> CPAN almost never installs non-Perl software.
>
> --keith
>
>
> --
> kkeller at wombat.san-francisco.ca.us
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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