BriXen Mac OS
sasha:~ brian$ rvm get head |
Original installed RVM version: |
rvm 1.8.4 by Wayne E. Seguin (wayneeseguin@gmail.com) [https://rvm.beginrescueend.com/] |
remote: Counting objects: 48, done. |
remote: Compressing objects: 100% (15/15), done. |
remote: Total 43 (delta 32), reused 39 (delta 28) |
Unpacking objects: 100% (43/43), done. |
From git://github.com/wayneeseguin/rvm |
* branch master -> FETCH_HEAD |
Updating 5b137ba.5ff8aca |
Fast-forward |
scripts/selector 2118 ++++++++++++++++++++++++++---------------------------- |
1 files changed, 1032 insertions(+), 1086 deletions(-) |
RVM: Shell scripts enabling management of multiple ruby environments. |
RTFM: https://rvm.beginrescueend.com/ |
HELP: http://webchat.freenode.net/?channels=rvm (#rvm on irc.freenode.net) |
Installing RVM to /Users/brian/.rvm/ |
Correct permissions for base binaries in /Users/brian/.rvm/bin.. |
Copying manpages into place. |
Notes for Darwin ( Mac OS X ) |
For Snow Leopard be sure to have Xcode Tools Version 3.2.1 (1613) or later |
You should download the latest Xcode tools from developer.apple.com. |
(This is since the dvd install for Snow Leopard contained bugs). |
If you intend on installing MacRuby you must install LLVM first. |
If you intend on installing JRuby you must install the JDK. |
If you intend on installing IronRuby you must install Mono |
(version 2.6 or greater is recommended). |
To use an RVM installed Ruby as default instead of the system ruby: |
rvm install 1.8.7 # installs patch 352: closest supported version |
rvm system ; rvm gemset export system.gems ; rvm 1.8.7 ; rvm gemset import system # migrate your gems |
rvm --default 1.8.7 |
NOTE: |
As of 1.8.0 RVM once again loads .rvmrc files, by default, after asking your |
permission to trust it of course. If you do not wish to be enabled, simply set: |
export rvm_project_rvmrc=0 |
Within either your /etc/rvmrc or $HOME/.rvmrc file. This will turn off the |
cd/pushd hooks when sourcing the rvm() function into your shell. |
Example: echo 'export rvm_project_rvmrc=0' >> $HOME/.rvmrc; |
(Then close the current shell and open a new one.) |
You must now complete the install by loading RVM in new shells. |
If you wish to use RVM in an interactive fashion in your shells then |
Place the following line at the end of your shell's loading files |
(.bashrc or .bash_profile for bash and .zshrc for zsh), |
after all PATH/variable settings: |
[[ -s '/Users/brian/.rvm/scripts/rvm' ]] && source '/Users/brian/.rvm/scripts/rvm' # This loads RVM into a shell session. |
You only need to add this line the first time you install RVM. |
If you are choosing to source RVM into your environment to switch current |
shell environments, be sure to close this shell and open a new one so that |
the RVM functions load. |
Installation of RVM to /Users/brian/.rvm/ is complete. |
Brian Ford, |
If you have any questions, issues and/or ideas for improvement please |
fork the project and issue a pull request. |
If you wish to disable the project .rvmrc file functionality, set |
rvm_project_rvmrc=0 in either /etc/rvmrc or ~/.rvmrc. |
Thank you for using RVM! |
I sincerely hope that RVM helps to make your life easier and more enjoyable!!! |
~Wayne |
Installed RVM HEAD version: |
rvm 1.8.4 by Wayne E. Seguin (wayneeseguin@gmail.com) [https://rvm.beginrescueend.com/] |
sasha:~ brian$ rvm reload |
RVM reloaded! |
sasha:~ brian$ rvm list |
rvm rubies |
rbx-head-1_9 [ x86_64 ] |
ruby-1.9.2-p180 [ x86_64 ] |
ruby-1.9.2-p290 [ x86_64 ] |
sasha:~ brian$ rvm remove rbx-head-1_9 |
ERROR: Unknown ruby interpreter string component: '1_9' |
ERROR: Cannot remove unknown package ' |
sasha:~ brian$ rm -rf ~/.rvm/help/ |
alias disk-usage gemset list rake rvmrc uninstall |
benchmark docs gemsets migrate remove snapshot update |
build exec get monitor repair specs upgrade |
cleanup fetch implode notes reset srcdir use |
current gem info package ruby tests wrapper |
debug gemdir install pkg rubygems tools |
sasha:~ brian$ rm -rf ~/.rvm/rubies/rbx-head-1_9/ |
.irbrc 18/ 19/ bin/ gems/ kernel/ lib/ man/ runtime/ |
sasha:~ brian$ rm -rf ~/.rvm/rubies/rbx* ~/.rvm/repos/rbx* ~/.rvm/src/rbx* ~/.rvm/gems/rbx* |
sasha:~ brian$ rvm install -n 1_9 rbx -- --default-version=1.9 |
rbx-head-1_9 installing #dependencies |
Cloning git://github.com/rubinius/rubinius.git |
Copying from repo to source.. |
rbx-head-1_9 - #configuring |
rbx-head-1_9 - #compiling |
rbx-head-1_9 - adjusting #shebangs for (erb ri rdoc). |
rbx-head-1_9 - #importing default gemsets (/Users/brian/.rvm/gemsets/) |
ERROR: Unknown ruby interpreter string component: '1_9' |
WARN: rbx is not installed. |
To install do: 'rvm install ' |
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posted by Valerie Obenchain, July 2014
Contents
- Software Infrastructure
- Education and Outreach
- Build System
- Resources, Courses and Conferences
Software Infrastructure
BSgenome
packages 2bit conversion
Current use cases for BSgenome packages emphasize quering many smallerregions across the entire genome, e.g., assembling many transcriptsequences from the underlying coding sequence genomic ranges. Toefficiently enable this use case, many BSgenome data packages are nowusing the UCSC 2bit format to store the sequences on disk.
One limitation of the 2bit format is that it does not support genomesthat contain letters other than As, Cs, Gs, Ts, or Ns. These genomes(e.g. hg17, hg18, GRCh38, Ecoli, TAIR.04232008, and TAIR.TAIR9) usethe previous .rda storage format, with fast whole-chromosome accessbut somewhat slower but still very usable random access.
The 2bit format is currently available in devel, but will be part ofthe next release of Bioconductor. Hervé and Martin worked onthis project with thanks to Michael for supporting the 2bit format inrtracklayer
.
S4 Vectors
package
In April Hervé started to split out the low level functions from IRanges
and move them to the new S4Vectors
package.IRanges
had grown to 90 classes, 157 generics and 844 methodsand was becoming difficult to maintain. The plan is to movecode that does not involve ranges, e.g., the Vector
andList
virtual classes, and DataFrame
, Rle
and Hits
concrete classes. This is a work in progress and estimated to be about 30% done.
pileups
Nate has been working on a pileup()
function which computespileup statistics in BAM files. Design goals were versatile record filtering and flexible presentation of results for downstream analyses. Filtering is achieved through the ScanBamParam
and PileupParam
objects; output is a data.frame
with variable columns based on the filtering applied.
pileup()
is available in the Rsamtools
package in devel. Other Bioconductor
packages that offer pileup-like functions include gmapR
(bam_tally), deepSNV
(bam2R) and Rsubread
(featureCounts). All have slightly different input requirements and output formats, see the man pages for details.
Git-SVN Bridge
The Bioconductor
project uses a Subversion (SVN) source controlsystem. SVN is effective for version control but does not offer social coding features such as GitHub’s issue tracking, pull requests or ease in granting permissions.
Broken Mac Screen Prank
In response to popular request, Dan created the Git-SVN Bridge to allow Github repositories to sync with the Bioconductor
SVN repository. Commits made in SVN are propagated to GitHub and vice versa. The service has been well received, with 73 bridges created as of June 2014.
To create a bridge see the Git-SVN Bridge HOWTO.
Bioconductor Amazon Machine Image (AMI)
The Bioconductor AMI has been overhauled and is now compatible withStarCluster. These enhancements makeit straightforward to spin up a cluster with nodes that communicate via MPI, SSH or Sun Grid Engine. Details available atthe AMI page.
The process of creating the AMI has been automated using Vagrantand Chef. Our scripts are publicly available,and can be used to provision an AMI, or a virtual machine (using Virtualbox or VMware) or even a physical machine.
Education and Outreach
Web site re-design
The Bioconductor
home page now has what we hope is a moreintuitive and user friendly interface. The ‘Install’, ‘Learn’, ‘Use’ and ‘Develop’ fields organize resources for the novice through the advanced developer.
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biocViews
Sonali continued her work on biocViews this quarter. A new function,recommendBiocViews()
is available in the biocViews
package. Thefunction looks at words in the DESCRIPTION, man pages and vignette,and suggests possible terms for use in the biocViews:
field ofpackage DESCRIPTION files. Los vegas slot. The function also identifies invalidbiocViews terms (e.g., mis-spellings) present in the packageDESCRIPTION file.
recommendBiocViews()
has been incorporated into the Single PackageBuilder that checks new package submissions; new package authors areencouraged to run it before submitting a package. Remember that biocViews are case-sensitive and branch-sensitive (i.e., terms for a Software package must come from the Software branch of biocViews).
Sonali distributed recommended views for all devel software packagesto the mailing list in June. For the complete list see thispost.
Instructional videos
We are looking into short, single-topic videos as an interactive complement to traditional vignettes and workflows.
The plan is to create a series of 5 minute videos that encapsulate a HOWTO skill or overview a project aspect. You can tour the website with Dan or do a ‘quick start’ with Martin’s overview of key packages and classes.Watch Marc slice and dice an AnnotationDb object or read BAM and VCF files with Sonali and Valerie.
Sonali and Martin have led this effort and plan to unveil the first videos at BioC 2014 in Boston.
Build System
Branching the experimental data Subversion repository
Historically, only the Subversion repository for the Bioconductor
softwarepackages had a distinct branch for each release. Subversion repositories forexperimental data and annotation packages had a trunk with no branches.
Starting with the Spring 2014 release a branch was created in the Subversionrepository for the experimental data. The motivation was to allow software and experimental data packages to evolve together in release and devel build environments. It was often the case that updates to a software package broke the companion experimental data. Changes made to the experimental data were committed to trunk and propagated to both release and devel builds creating incompatibilities in one place or the other.
A consequence of creating the new branch is the need to bump ‘y’ ofthe ‘x.y.z’ version numbering scheme at release time (as we do for software). The Annotations have not changed; they are not under Subversion, do not go through automated builds and do not have a version policy.
Changes in how the experimental data Subversion repository is manged are relevant for developers only. The public repositories remain the same with a separate repository for each Bioconductor
version. There is no visible change for users accessing the public repositories.
New Mac OS X Mavericks build machines
An R
3.1.0 binary for Mac OS X 10.9 (Mavericks) is now available fromR Core. This R
as been built with Xcode 5 to leverage new compilers and functionalities in Mavericks not available in earlier OS X versions.
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To provide compatible Bioconductor
package binaries we needed newbuild machines. Dan has configured two new Mavericks, one in release(morelia) and one in devel(oaxaca).
The introduction of Xcode and the clang compiler resulted in new errors for packages with C and C++ code. Nate and Dan spent manyhours troubleshooting with package authors and came up with a list of common problems and solutions. Lessons learned were distilled into the C++/Mavericks Best Practicesdocument.
Quarterly Project Statistics
There were 86953 downloads of Bioconductor
software packagesover the past quarter (April - June). During this time 41 new software packages were accepted. A full summary of package download stats isavailable here.
Hoe down throw down mac os. The web site saw approximately 119,000 visitors (26% increase from the previous year) from 180 countries, with the US, China, United Kingdom, Germany, and Canada at the head of the pack.
Resources, Courses and Conferences
Data Analysis for Genome Biology (CSAMA)
This one week intensive course is offered each year in Brixen-Bressanone,Italy and focuses on statistical and computational analysis of large-scale biological experiments. The course is intended for researchers with basic familiarity with the experimental technologies and who are interested in developing their own advanced data analyses.
Topics this year included RNASeq differential expression, variant calling and ChIP-Seq as well as the essentials of statistical testing, machine learning, visualization and of course using R. Michael Lawrence presented a Scalable Genomics
lab which covered topics of limiting resource consumption, using iteration when appropriate, and scaling genome graphics. Much of the material is based on a manuscriptcurrently in press at the journal Statistical Science.
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Materials from the June 2014 course are available on the web.
Community Resources
New Community Resources linksinclude the book and lab from MOOC: PH525x Data Analysis for Genomics.This online course was offered in April 2014 by Rafael Irizarry and Michael Love. Course goals were to enable students to analyze and interpret data generated by modern genomics technology, specifically microarray and next generation sequencing. Applications included gene expression, association of genomic variants to disease, and measuring epigenetic marks.
Also on the Community page are links to YouTube videos made by communitymembers, tips on getting started with R/Bioconductor by Thomas Girke, analysis of 23andme data by Vince Buffalo and Sean Davis’ R/Bioconductor blog.
BioC 2014
The annual meeting is in Boston this year (July 30 - August 1). See theweb sitefor a list of speakers and workshops.
Please send comments or questions to Valerie at vobencha@fhcrc.org.