<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43120?offset=50 https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics Sat, 31 May 2014 15:41:16 -0500 https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics <![CDATA[Linux Sort Commands for Bioinformatics]]> Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.

sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
sort input.txt

sort a huge file (GNU sort ONLY):
sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

sort starting from the third column, skipping the first two columns:
sort +2 input.txt

sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
sort -k2,2nr -k3,3 input.txt

sort starting from the 4th character at column 2, as numbers:
sort -k2.4n input.txt

More Linxu sort command information

If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

man sort

or

sort --help

on your Unix/Linux system.

]]> Rahul Nayak https://bioinformaticsonline.com/pages/view/27965/cheatsheet-for-linux Wed, 22 Jun 2016 07:55:06 -0500 https://bioinformaticsonline.com/pages/view/27965/cheatsheet-for-linux <![CDATA[Cheatsheet for Linux !!]]> Linux Commands Cheat Sheet

    File System

    ls — list items in current directory

    ls -l — list items in current directory and show in long format to see perimissions, size, an modification date

    ls -a — list all items in current directory, including hidden files

    ls -F — list all items in current directory and show directories with a slash and executables with a star

    ls dir — list all items in directory dir

    cd dir — change directory to dir

    cd .. — go up one directory

    cd / — go to the root directory

    cd ~ — go to to your home directory

    cd - — go to the last directory you were just in

    pwd — show present working directory

    mkdir dir — make directory dir

    rm file — remove file

    rm -r dir — remove directory dir recursively

    cp file1 file2 — copy file1 to file2

    cp -r dir1 dir2 — copy directory dir1 to dir2 recursively

    mv file1 file2 — move (rename) file1 to file2

    ln -s file link — create symbolic link to file

    touch file — create or update file

    cat file — output the contents of file

    less file — view file with page navigation

    head file — output the first 10 lines of file

    tail file — output the last 10 lines of file

    tail -f file — output the contents of file as it grows, starting with the last 10 lines

    vim file — edit file

    alias name 'command' — create an alias for a command
    System

    shutdown — shut down machine

    reboot — restart machine

    date — show the current date and time

    whoami — who you are logged in as

    finger user — display information about user

    man command — show the manual for command

    df — show disk usage

    du — show directory space usage

    free — show memory and swap usage

    whereis app — show possible locations of app

    which app — show which app will be run by default
    Process Management

    ps — display your currently active processes

    top — display all running processes

    kill pid — kill process id pid

    kill -9 pid — force kill process id pid
    Permissions

    ls -l — list items in current directory and show permissions

    chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.

    7 — full permissions

    6 — read and write only

    5 — read and execute only

    4 — read only

    3 — write and execute only

    2 — write only

    1 — execute only

    0 — no permissions

    chmod 600 file — you can read and write - good for files

    chmod 700 file — you can read, write, and execute - good for scripts

    chmod 644 file — you can read and write, and everyone else can only read - good for web pages

    chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
    Networking

    wget file — download a file

    curl file — download a file

    scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine

    scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server

    scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine

    ssh user@host — connect to host as user

    ssh -p port user@host — connect to host on port as user

    ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login

    ping host — ping host and output results

    whois domain — get information for domain

    dig domain — get DNS information for domain

    dig -x host — reverse lookup host

    lsof -i tcp:1337 — list all processes running on port 1337
    Searching

    grep pattern files — search for pattern in files

    grep -r pattern dir — search recursively for pattern in dir

    grep -rn pattern dir — search recursively for pattern in dir and show the line number found

    grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension

    command | grep pattern — search for pattern in the output of command

    find file — find all instances of file in real system

    locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find

    sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
    Compression

    tar cf file.tar files — create a tar named file.tar containing files

    tar xf file.tar — extract the files from file.tar

    tar czf file.tar.gz files — create a tar with Gzip compression

    tar xzf file.tar.gz — extract a tar using Gzip

    gzip file — compresses file and renames it to file.gz

    gzip -d file.gz — decompresses file.gz back to file
    Shortcuts

    ctrl+a — move cursor to beginning of line

    ctrl+f — move cursor to end of line

    alt+f — move cursor forward 1 word

    alt+b — move cursor backward 1 word

]]> Jit https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty Tue, 08 May 2018 08:03:21 -0500 https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty <![CDATA[Installing Bandage on Ubunty !]]> The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04:

  1. Ensure the package lists are up-to-date: sudo apt-get update
  2. Install prerequisite packages: sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
  3. Download the Bandage code from GitHub: git clone https://github.com/rrwick/Bandage.git
  4. Open a terminal in the Bandage directory.
  5. Set the environment variable to specify that you will be using Qt 5, not Qt 4: export QT_SELECT=5
  6. Run qmake to generate a Makefile: qmake
  7. Build the program: make
  8. Bandage should now be an executable file.
  9. Optionally, copy the program into /usr/local/bin: sudo make install. The Bandage build directory can then be deleted.

➜ Tools git:(master) ✗ sudo apt-get update
[sudo] password for urbe: 
Hit:1 http://ppa.launchpad.net/webupd8team/atom/ubuntu xenial InRelease
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Hit:4 http://be.archive.ubuntu.com/ubuntu xenial InRelease 
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Get:7 https://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease [3.590 B] 
Hit:8 https://download.docker.com/linux/ubuntu xenial InRelease 
Ign:9 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ InRelease 
Hit:10 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ Release 
Get:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease [6.372 B]
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Err:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease 
The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
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Fetched 4.779 kB in 2s (1.606 kB/s) 
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
W: Failed to fetch http://packages.cloud.google.com/apt/dists/cloud-sdk-xenial/InRelease The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
W: Some index files failed to download. They have been ignored, or old ones used instead.
➜ Tools git:(master) ✗ sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
Reading package lists... Done
Building dependency tree 
Reading state information... Done
build-essential is already the newest version (12.1ubuntu2).
git is already the newest version (1:2.7.4-0ubuntu1.3).
The following packages were automatically installed and are no longer required:
bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic
linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic linux-signed-image-4.4.0-116-generic runc ubuntu-fan
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5
libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5test5 libqt5widgets5 libqt5xml5 libwayland-bin
libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0-dev
libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev qt5-qmake
qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
Suggested packages:
libqt5libqgtk2 qt5-image-formats-plugins qtwayland5 libxext-doc libmysqlclient-dev libpq-dev libsqlite3-dev unixodbc-dev
The following NEW packages will be installed:
libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5
libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5widgets5 libqt5xml5
libwayland-bin libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0
libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev
qt5-qmake qtbase5-dev qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
0 upgraded, 64 newly installed, 0 to remove and 11 not upgraded.
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➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Bandage.git
Cloning into 'Bandage'...
remote: Counting objects: 7813, done.
remote: Total 7813 (delta 0), reused 0 (delta 0), pack-reused 7813
Receiving objects: 100% (7813/7813), 27.43 MiB | 16.33 MiB/s, done.
Resolving deltas: 100% (5973/5973), done.
Checking connectivity... done.
➜ Tools git:(master) ✗ cd Bandage 
➜ Bandage git:(master) ls
Bandage.pro BandageTests.pro blast build_scripts command_line COPYING graph images ogdf program README.md tests ui
➜ Bandage git:(master) export QT_SELECT=5
➜ Bandage git:(master) qmake
➜ Bandage git:(master) ✗ make
/home/urbe/anaconda3/bin/uic ui/mainwindow.ui -o ui_mainwindow.h
/home/urbe/anaconda3/bin/uic ui/settingsdialog.ui -o ui_settingsdialog.h
/home/urbe/anaconda3/bin/uic ui/aboutdialog.ui -o ui_aboutdialog.h
/home/urbe/anaconda3/bin/uic ui/enteroneblastquerydialog.ui -o ui_enteroneblastquerydialog.h
/home/urbe/anaconda3/bin/uic ui/blastsearchdialog.ui -o ui_blastsearchdialog.h
/home/urbe/anaconda3/bin/uic ui/myprogressdialog.ui -o ui_myprogressdialog.h
/home/urbe/anaconda3/bin/uic ui/pathspecifydialog.ui -o ui_pathspecifydialog.h
/home/urbe/anaconda3/bin/uic ui/querypathsdialog.ui -o ui_querypathsdialog.h
/home/urbe/anaconda3/bin/uic ui/blasthitfiltersdialog.ui -o ui_blasthitfiltersdialog.h
/home/urbe/anaconda3/bin/uic ui/changenodenamedialog.ui -o ui_changenodenamedialog.h
/home/urbe/anaconda3/bin/uic ui/graphinfodialog.ui -o ui_graphinfodialog.h
/home/urbe/anaconda3/bin/uic ui/changenodedepthdialog.ui -o ui_changenodedepthdialog.h
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o main.o program/main.cpp
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o settings.o program/settings.cpp
....

...
g++ -Wl,-O1 -Wl,-rpath,/home/urbe/anaconda3/lib -o Bandage main.o settings.o globals.o graphlayoutworker.o debruijnnode.o debruijnedge.o graphicsitemnode.o graphicsitemedge.o mainwindow.o graphicsviewzoom.o settingsdialog.o mygraphicsview.o mygraphicsscene.o aboutdialog.o enteroneblastquerydialog.o blasthit.o blastqueries.o blastsearchdialog.o infotextwidget.o assemblygraph.o verticalscrollarea.o myprogressdialog.o nodewidthvisualaid.o verticallabel.o load.o image.o commoncommandlinefunctions.o mytablewidget.o buildblastdatabaseworker.o colourbutton.o blastquery.o runblastsearchworker.o blastsearch.o path.o pathspecifydialog.o graphlocation.o tablewidgetitemint.o tablewidgetitemdouble.o tablewidgetitemshown.o memory.o querypathspushbutton.o querypathsdialog.o blastquerypath.o blasthitfiltersdialog.o scinot.o changenodenamedialog.o querypathsequencecopybutton.o querypaths.o info.o reduce.o Graph.o GraphAttributes.o FMMMLayout.o geometry.o ClusterGraphAttributes.o FruchtermanReingold.o NMM.o GmlParser.o simple_graph_alg.o basic.o XmlParser.o String.o Hashing.o PoolMemoryAllocator.o GraphCopy.o CombinatorialEmbedding.o OgmlParser.o ClusterGraph.o Math.o EdgeAttributes.o NodeAttributes.o MAARPacking.o Multilevel.o numexcept.o Set.o Ogml.o DinoXmlParser.o DinoXmlScanner.o DinoTools.o DinoLineBuffer.o System.o QuadTreeNM.o QuadTreeNodeNM.o Constraint.o MultilevelGraph.o graphinfodialog.o tablewidgetitemname.o changenodedepthdialog.o qrc_images.o moc_graphlayoutworker.o moc_mainwindow.o moc_graphicsviewzoom.o moc_settingsdialog.o moc_mygraphicsview.o moc_mygraphicsscene.o moc_aboutdialog.o moc_enteroneblastquerydialog.o moc_blastquery.o moc_blastsearchdialog.o moc_infotextwidget.o moc_assemblygraph.o moc_verticalscrollarea.o moc_myprogressdialog.o moc_nodewidthvisualaid.o moc_verticallabel.o moc_mytablewidget.o moc_buildblastdatabaseworker.o moc_colourbutton.o moc_runblastsearchworker.o moc_pathspecifydialog.o moc_querypathspushbutton.o moc_querypathsdialog.o moc_blasthitfiltersdialog.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.o moc_graphinfodialog.o moc_changenodedepthdialog.o -L/usr/lib -L/home/urbe/anaconda3/lib -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread 
➜ Bandage git:(master) ✗ ls 
aboutdialog.o DinoTools.o Makefile moc_infotextwidget.cpp moc_verticalscrollarea.o scinot.o
assemblygraph.o DinoXmlParser.o Math.o moc_infotextwidget.o MultilevelGraph.o Set.o
Bandage DinoXmlScanner.o memory.o moc_mainwindow.cpp Multilevel.o settingsdialog.o
Bandage.pro EdgeAttributes.o moc_aboutdialog.cpp moc_mainwindow.o mygraphicsscene.o settings.o
BandageTests.pro enteroneblastquerydialog.o moc_aboutdialog.o moc_mygraphicsscene.cpp mygraphicsview.o simple_graph_alg.o
basic.o FMMMLayout.o moc_assemblygraph.cpp moc_mygraphicsscene.o myprogressdialog.o String.o
blast FruchtermanReingold.o moc_assemblygraph.o moc_mygraphicsview.cpp mytablewidget.o System.o
blasthitfiltersdialog.o geometry.o moc_blasthitfiltersdialog.cpp moc_mygraphicsview.o NMM.o tablewidgetitemdouble.o
blasthit.o globals.o moc_blasthitfiltersdialog.o moc_myprogressdialog.cpp NodeAttributes.o tablewidgetitemint.o
blastqueries.o GmlParser.o moc_blastquery.cpp moc_myprogressdialog.o nodewidthvisualaid.o tablewidgetitemname.o
blastquery.o graph moc_blastquery.o moc_mytablewidget.cpp numexcept.o tablewidgetitemshown.o
blastquerypath.o GraphAttributes.o moc_blastsearchdialog.cpp moc_mytablewidget.o ogdf tests
blastsearchdialog.o GraphCopy.o moc_blastsearchdialog.o moc_nodewidthvisualaid.cpp Ogml.o ui
blastsearch.o graphicsitemedge.o moc_buildblastdatabaseworker.cpp moc_nodewidthvisualaid.o OgmlParser.o ui_aboutdialog.h
buildblastdatabaseworker.o graphicsitemnode.o moc_buildblastdatabaseworker.o moc_pathspecifydialog.cpp path.o ui_blasthitfiltersdialog.h
build_scripts graphicsviewzoom.o moc_changenodedepthdialog.cpp moc_pathspecifydialog.o pathspecifydialog.o ui_blastsearchdialog.h
changenodedepthdialog.o graphinfodialog.o moc_changenodedepthdialog.o moc_querypathsdialog.cpp PoolMemoryAllocator.o ui_changenodedepthdialog.h
changenodenamedialog.o graphlayoutworker.o moc_changenodenamedialog.cpp moc_querypathsdialog.o program ui_changenodenamedialog.h
ClusterGraphAttributes.o graphlocation.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.cpp qrc_images.cpp ui_enteroneblastquerydialog.h
ClusterGraph.o Graph.o moc_colourbutton.cpp moc_querypathsequencecopybutton.o qrc_images.o ui_graphinfodialog.h
colourbutton.o Hashing.o moc_colourbutton.o moc_querypathspushbutton.cpp QuadTreeNM.o ui_mainwindow.h
CombinatorialEmbedding.o image.o moc_enteroneblastquerydialog.cpp moc_querypathspushbutton.o QuadTreeNodeNM.o ui_myprogressdialog.h
command_line images moc_enteroneblastquerydialog.o moc_runblastsearchworker.cpp querypathsdialog.o ui_pathspecifydialog.h
commoncommandlinefunctions.o info.o moc_graphicsviewzoom.cpp moc_runblastsearchworker.o querypathsequencecopybutton.o ui_querypathsdialog.h
Constraint.o infotextwidget.o moc_graphicsviewzoom.o moc_settingsdialog.cpp querypaths.o ui_settingsdialog.h
COPYING load.o moc_graphinfodialog.cpp moc_settingsdialog.o querypathspushbutton.o verticallabel.o
debruijnedge.o MAARPacking.o moc_graphinfodialog.o moc_verticallabel.cpp README.md verticalscrollarea.o
debruijnnode.o main.o moc_graphlayoutworker.cpp moc_verticallabel.o reduce.o XmlParser.o
DinoLineBuffer.o mainwindow.o moc_graphlayoutworker.o moc_verticalscrollarea.cpp runblastsearchworker.o
➜ Bandage git:(master) ✗ ./Bandage

]]> Jit https://bioinformaticsonline.com/pages/view/37677/installing-blat-on-linux Tue, 11 Sep 2018 08:17:35 -0500 https://bioinformaticsonline.com/pages/view/37677/installing-blat-on-linux <![CDATA[Installing BLAT on Linux !]]> It's been a while since I last installed BLAT and when I went to the download directory at UCSC: http://users.soe.ucsc.edu/~kent/src/ I found that the latest blast is now version 35 and that the code to download was: blatSrc35.zip. However, you can also get pre-compiled binaries at: http://hgdownload.cse.ucsc.edu/admin/exe/ and that there was a linux x86_64 executable for my architecture available at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/. Though YYMV, BLAT can be a little bit of a tricky beast to get going, so I decided to download the source code and compile that.

I will be compiling this code as 'root' as a system tool in /usr/local/src, so do not scream at me for that.

First I created an /usr/local/src/blat directory and I copied the blatSrc35.zip file into that.

Next I used

unzip blatSrc35.zip

to unpack the archive. This gives a directory blatSrc now move into that directory.

#cd blatSrc

before you begin read the README file that comes with the source code.

One thing about building blat is that you need to set the MACHTYPE variable so that the BLAT sources know what type of machine you are compiling the software on.

on most *nix machines, typing

echo $MACHTYPE

will return the machine architecture type.

On my CentOS 6 based system this gave:

x86_64-redhat-linux-gnu

However, what BLAT requires is the 'short value' (ie the first part of the MACHTYPE). To correct this, in the bash shell type (change this to the correct MACHTYPE for your system)

MACHTYPE=x86_64
export MACHTYPE

now running the command:

echo $MACHTYPE

should give the correct short form of the MACHTYPE:

x86_64

now create the directory lib/$MACHTYPE in the source tree. ie:

mkdir lib/$MACHTYPE

For my machine, lib/x86_64 already existed, so I did not have to do this, but this is not the case for all architectures.

The BLAT code assumes that you are compiling BLAT as a non-privileged (ie non-root) user. As a result, you must create the directory for the executables to go into:

mkdir ~/bin/$MACHTYPE

If you are installing as a normal user, edit your .bashrc to add the following (change the x86_64 to be your MACHTYPE):

export PATH=~/bin/x86_64::$PATH

For me, though, this was not good enough. I wanted the executables in /usr/local/bin where all my other code goes. As a result I did some hackery...

There is a master make template in the inc directory called common.mk and I edited this file with the command:

vi inc/common.mk

I replaced the line

    BINDIR=${HOME}/bin/${MACHTYPE}

with

    BINDIR=/usr/local/bin

saved and quit (as this is in my path, I do not need to do anything else)

All the preparation is now done and you can create the blat executables by going into the toplevel of the blat source tree (for me it was /usr/local/src/blat/blatSrc, but change to wherever you unpacked blat into).

Now simply run the command:

make

to compile the code.

Blat installed cleanly and the executables were all neatly placed in /usr/local/bin/x86_64, just like I wanted.

now simply running the command:

blat

on the command line gives me information on blat and sample usage.

Blat is installed and it's installed properly in my system code tree!!!

]]> BioStar https://bioinformaticsonline.com/blog/view/43911/slurm-commands Wed, 06 Jul 2022 07:40:07 -0500 https://bioinformaticsonline.com/blog/view/43911/slurm-commands <![CDATA[SLURM Commands]]> SLURM commands

The following table shows SLURM commands on the SOE cluster.

CommandDescription
sbatch Submit batch scripts to the cluster
scancel Signal jobs or job steps that are under the control of Slurm.
sinfo View information about SLURM nodes and partitions.
squeue View information about jobs located in the SLURM scheduling queue
smap Graphically view information about SLURM jobs, partitions, and set configurations parameters
sqlog View information about running and finished jobs
sacct View resource accounting information for finished and running jobs
sstat View resource accounting information for running jobs

For more information, run man on the commands above. See some examples below.

1. Info about the partitions and nodes
List all the partitions available to you and the nodes therein:

sinfo

Nodes in state idle can accept new jobs.

Show a partition configuratuin, for example, SOE_main

scontrol show partition=SOE_main

Show current info about a specific node:

scontrol show node=<nodename>

You can also specify a group of nodes in the command above. For example, if your MPI job is running across soenode05,06,35,36, you can execute the command below to get the info on the nodes you are interested in:

scontrol show node=soenode[05-06,35-36]

An informative parameter in the output to look at would be CPULoad. It allows you to see how your application utilizes the CPUs on the running nodes.

2. Submit scripts
The header in a submit script specifies job name, partition (queue), time limit, memory allocation, number of nodes, number of cores, and files to collect standard output and error at run time, for example

#!/bin/bash

#SBATCH --job-name=OMP_run     # job name, "OMP_run"
#SBATCH --partition=SOE_main   # partition (queue)
#SBATCH -t 0-2:00              # time limit: (D-HH:MM) 
#SBATCH --mem=32000            # memory per node in MB 
#SBATCH --nodes=1              # number of nodes
#SBATCH --ntasks-per-node=16   # number of cores
#SBATCH --output=slurm.out     # file to collect standard output
#SBATCH --error=slurm.err      # file to collect standard errors

If the time limit is not specified in the submit script, SLURM will assign the default run time, 3 days. This means the job will be terminated by SLURM in 72 hrs. The maximum allowed run time is two weeks, 14-0:00.
If the memory limit is not requested, SLURM will assign the default 16 GB. The maximum allowed memory per node is 128 GB. To see how much RAM per node your job is using, you can run commands sacct or sstat to query MaxRSS for the job on the node - see examples below.
Depending on a type of application you need to run, the submit script may contain commands to create a temporary space on a computational node - see the discussion about using the file systems on the cluster.
Then it sets the environment specific to the application and starts the application on one or multiple nodes - see sbatch sample scripts in directory /usr/local/Samples on soemaster1.hpc.rutgers.edu.
You can submit your job to the cluster with sbatch command:

sbatch myscript.sh


3. Query job information
List all currently submitted jobs in running and pending states for a user:

squeue -u <username>

Command squeue can be run with format options to expose specific information, for example, when pending job #706 is scheduled to start running:

squeue -j 706 --format="%S"

START_TIME
2015-04-30T09:54:32

More info can be shown by placing additional format options, for example:

squeue -j 706 --format="%i %P %j %u %T %l %C %S"

JOBID PARTITION   NAME    USER STATE   TIMELIMIT  CPUS START_TIME
706   SOE_main  Par_job_3 mike PENDING 3-00:00:00 64   2015-04-30T09:54:32

To see when all the jobs, pending in the queue, are scheduled to start:

squeue --start


List all running and completed jobs for a user

sqlog -u <username>

or

sqlog -j <JobID>

The following appreviations are used for the job states:

       CA   CANCELLED      Job was cancelled.

       CD   COMPLETED      Job completed normally.

       CG   COMPLETING     Job is in the process of completing.

       F    FAILED         Job termined abnormally.

       NF   NODE_FAIL      Job terminated due to node failure.

       PD   PENDING        Job is pending allocation.

       R    RUNNING        Job currently has an allocation.

       S    SUSPENDED      Job is suspended.

       TO   TIMEOUT        Job terminated upon reaching its time limit.

You can specify the fields you would like to see in the output of sqlog:

sqlog --format=list

The command below, for example, provides Job ID, user name, exit state, start date-time, and end date-time for job #2831:

sqlog -j 2831 --format=jid,user,state,start,end

List status info for a currently running job:

sstat -j <jobid>

A formatted output can be used to gain only a specific info, for example, the maximum resident RAM usage on a node:

sstat --format="JobID,MaxRSS" -j <jobid>

To get statistics on completed jobs by jobID:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -j <jobid>

To view the same information for all jobs of a user:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -u <username>

To print a list of fields that can be specified with the --format option:

sacct --helpformat

For example, to get Job ID, Job name, Exit state, start date-time, and end date-time for job #2831:

sacct -j 2831 --format="JobID,JobName,State,Start,End"

Another useful command to gain information about a running job is scontrol:

scontrol show job=<jobid>


4. Cancel a job
To cancel one job:

scancel <jobid>

To cancel one job and delete the TMP directory created by the submit script on a node:

sdel <jobid>

To cancel all the jobs for a user:

scancel -u <username>

To cancel one or more jobs by name:

scancel --name <myJobName>
]]> Shruti Paniwala https://bioinformaticsonline.com/opportunity/view/40868/inrae-organises-open-competitions-to-recruit-research-scientists-on-permanent-positions Sun, 02 Feb 2020 23:08:36 -0600 <![CDATA[INRAE organises open competitions to recruit research scientists on permanent positions.]]> Each year, INRAE organises open competitions to recruit research scientists on permanent positions. The recruitment campaign is generally aimed at researchers who have recently obtained their PhD. Candidates are recruited on the basis of their scientific competence which they will put to the service of INRAE's major research axes by responding to a research topic. Candidates must have published articles on the results of their PhD.

Campaign calendar:

- Opening date for applications: January 30, 2020
- Deadline for applications: March 5, 2020
- Pre-selections: April-May 2020
- Final selections: May-June 2020
- Starting date for appointments: from September 2020

More at https://jobs.inrae.fr/en/open-competitions/open-competions-research-scientists-crcn

]]> https://bioinformaticsonline.com/opportunity/view/43768/summer-school-open-to-phd-students Wed, 02 Feb 2022 06:08:35 -0600 <![CDATA[Summer school open to PhD students]]> Some PhD students are organizing a summer school open to PhD students with different backgrounds and interests.

Several sessions and workshops will be held within five focus groups, and one common theme: mountain research.

The summer school will take place in Obergurgl, in the middle of the Austrian Alps, September 5-9.

Abstract submission is now open, until February 16th: https://www.imc2022.info/summerschool/

The summer school takes place in the context of the International Mountain Conference 2022, Innsbruck, Austria: https://www.imc2022.info/

Please feel free to spread the word among potentially interested colleagues and PhD students.

"Capponi, Lisa"

]]> https://bioinformaticsonline.com/blog/view/37000/install-imagemagick-from-unix-source Wed, 20 Jun 2018 11:22:43 -0500 https://bioinformaticsonline.com/blog/view/37000/install-imagemagick-from-unix-source <![CDATA[Install ImageMagick from Unix Source]]> ImageMagick builds on a variety of Unix and Unix-like operating systems including Linux, Solaris, FreeBSD, Mac OS X, and others. A compiler is required and fortunately almost all modern Unix systems have one. Download ImageMagick.tar.gzfrom www.imagemagick.org or a mirrors and verify its message digest.

Unpack the distribution with this command:

tar xvzf ImageMagick.tar.gz

Next configure and compile ImageMagick. Note the pkg-config script is required so that ImageMagick can find certain optional delegate libraries on your system. To configure, type:

$ cd ImageMagick-7.0.8
$ ./configure
$ make

If ImageMagick configured and compiled without complaint, you are ready to install it on your system. Administrator privileges are required to install. To install, type

sudo make install

You may need to configure the dynamic linker run-time bindings:

sudo ldconfig /usr/local/lib

Finally, verify the ImageMagick install worked properly, type

/usr/local/bin/convert logo: logo.gif

For a more comprehensive test, run the ImageMagick validation suite. Ghostscript is a prerequisite, otherwise the EPS, PS, and PDF tests will fail.

make check

Congratulations, you have a working ImageMagick distribution and you are ready to use ImageMagick to convert, compose, or edit your images or perhaps you'll want to use one of the Application Program Interfaces for C, C++, Perl, and others.

The above instructions will satisfy a great number of ImageMagick users, but we suspect a few will have additional questions or problems to consider. For example, what does one do if ImageMagick fails to configure or compile? Or what if you don't have administrator privileges and what if you don't want to install ImageMagick in the default /../usr/local folder? You will find the answer to these questions, and more, in Advanced Unix Source Installation.

jitendra@jitendra-UNLOCK-INSTALL[Downloads] git clone https://github.com/ImageMagick/ImageMagick.git []
Cloning into 'ImageMagick'...
remote: Counting objects: 124593, done.
remote: Compressing objects: 100% (77/77), done.
remote: Total 124593 (delta 94), reused 94 (delta 64), pack-reused 124452
Receiving objects: 100% (124593/124593), 76.94 MiB | 24.07 MiB/s, done.
Resolving deltas: 100% (106498/106498), done.
Checking connectivity... done.
jitendra@jitendra-UNLOCK-INSTALL[Downloads] cd ImageMagick []
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] make []
make: *** No targets specified and no makefile found. Stop.
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] ./configure []
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1000' is supported by ustar format... yes
checking whether GID '1000' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
configuring ImageMagick 7.0.8-3
checking whether build environment is sane... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking how to print strings... printf
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for gcc option to accept ISO C99... (cached) none needed
checking CFLAGS for maximum warnings... -Wall
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... (cached) /bin/sed
checking for gawk... (cached) gawk
checking if malloc debugging is wanted... no
checking for __attribute__... yes
checking for C compiler vendor... gnu
checking for gcc architecture flag...
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306a9:3100800:7fbae3ff:bfebfbff
checking whether C compiler accepts -mtune=ivybridge... yes
checking for gcc architecture flag... -mtune=ivybridge
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.20... yes
checking size of size_t... 8
checking for C compiler vendor... (cached) gnu
./configure: line 9486: AX_COMPILER_FLAGS: command not found
checking CFLAGS for maximum warnings... (cached) -Wall
checking if LD -Wl,--version-script works... yes
checking for linker lazyload option... none
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for gcc option to support OpenMP... -fopenmp
checking for pthread_join using gcc -pthread ... yes
checking whether gcc is Clang... (cached) no
checking for joinable pthread attribute... (cached) PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... (cached) no
checking for PTHREAD_PRIO_INHERIT... (cached) yes
checking whether we are using the Microsoft C compiler... no
checking CL/cl.h usability... no
checking CL/cl.h presence... no
checking for CL/cl.h... no
checking OpenCL/cl.h usability... no
checking OpenCL/cl.h presence... no
checking for OpenCL/cl.h... no
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenCL library... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether to enable maintainer-specific portions of Makefiles... no
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checking arm/limits.h usability... no
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checking sys/wait.h usability... yes
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checking for stdbool.h that conforms to C99... yes
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checking for preprocessor stringizing operator... yes
checking whether stat file-mode macros are broken... no
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct tm.tm_zone... yes
checking whether #! works in shell scripts... yes
checking whether char is unsigned... no
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checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking for working volatile... (cached) yes
checking whether byte ordering is bigendian... no
checking for int8_t... yes
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checking for unsigned long long int... yes
checking for long long int... yes
checking for intmax_t... yes
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checking for long double... yes
checking for long double with more range or precision than double... yes
checking for long long int... (cached) yes
checking for mbstate_t... yes
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checking for uid_t in sys/types.h... yes
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checking for unsigned long long int... (cached) yes
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checking size of float_t... 4
checking size of double_t... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of signed short... 2
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checking size of signed long... 8
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checking size of ssize_t... 8
checking size of unsigned int*... 8
checking for signed 8-bit type... signed char
checking for unsigned 8-bit type... unsigned char
checking for signed 16-bit type... signed short
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checking for signed 32-bit type... signed int
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checking for signed 64-bit type... signed long
checking for unsigned 64-bit type... unsigned long
checking for unsigned maximum type... unsigned long
checking for pointer difference type... unsigned long
checking whether our compiler supports __func__... yes
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checking vfork.h usability... no
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checking for fork... yes
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checking for working fork... yes
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checking for working memcmp... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
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checking for sys/socket.h... (cached) yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking return type of signal handlers... void
checking for working strtod... yes
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checking whether strerror_r returns char *... yes
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checking for ftruncate... yes
checking for getc_unlocked... yes
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checking for getexecname... no
checking for getdtablesize... yes
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checking for gmtime_r... yes
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checking for j0... yes
checking for j1... yes
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checking for seekdir... yes
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checking for socket... yes
checking for sqrt... yes
checking for setvbuf... yes
checking for stat... yes
checking for strchr... yes
checking for strrchr... yes
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checking for strpbrk... yes
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checking for strtod... (cached) yes
checking for strtod_l... yes
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checking for strtoul... yes
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checking for sigaction... yes
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checking for library containing clock_gettime... none required
checking whether clock_gettime supports CLOCK_REALTIME... yes
checking whether pread is declared... yes
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checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking whether the compiler recognizes bool as a built-in type... yes
checking whether the compiler implements namespaces... yes
checking if g++ supports namespace std... yes
checking whether the compiler supports ISO C++ standard library... yes
checking for g++ option to support OpenMP... -fopenmp
checking whether C++ compiler is sufficient for Magick++... yes
checking for X11 configure files...
checking for GOMP_parallel_start in -lgomp... yes
-------------------------------------------------------------
checking for BZLIB...
checking bzlib.h usability... no
checking bzlib.h presence... no
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checking if BZLIB package is complete... no
checking for X... libraries , headers
checking for gethostbyname... yes
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checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
-------------------------------------------------------------
checking for X11...
checking for shmctl... yes
checking for XShmAttach in -lXext... yes
checking for XShapeCombineMask in -lXext... yes
checking for XtSetEventDispatcher in -lXt... yes
-------------------------------------------------------------
checking for ZLIB... yes

-------------------------------------------------------------
checking for DPS...
checking DPS/dpsXclient.h usability... no
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checking for XDPSPixelsPerPoint in -ldpstk... no
checking if DPS package is complete... no
-------------------------------------------------------------
checking for fftw3... no

-------------------------------------------------------------
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checking flif.h usability... no
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-------------------------------------------------------------
checking for FlashPIX...
checking fpxlib.h usability... no
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checking for FPX_OpenImageByFilename in -lfpx... no
checking if FlashPIX package is complete... no
-------------------------------------------------------------
checking for ddjvuapi... no

-------------------------------------------------------------
checking for FONTCONFIG... yes

-------------------------------------------------------------
checking for FREETYPE... yes

-------------------------------------------------------------
checking for RAQM... no

-------------------------------------------------------------
checking for GVC... no

-------------------------------------------------------------
checking for HEIF... no

-------------------------------------------------------------
checking for JBIG...
checking jbig.h usability... yes
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-------------------------------------------------------------
checking for JPEG...
checking jconfig.h usability... yes
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checking jerror.h usability... yes
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checking jmorecfg.h usability... yes
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checking jpeglib.h usability... yes
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checking for jpeg_read_header in -ljpeg... yes
checking for JPEG library is version 6b or later... yes
checking if JPEG package is complete... yes
-------------------------------------------------------------
checking for LCMS2... no

-------------------------------------------------------------
checking for LIBOPENJP2... no

-------------------------------------------------------------
checking for LQR... no

-------------------------------------------------------------
checking for LZMA... yes

-------------------------------------------------------------
checking for OPENEXR... no

-------------------------------------------------------------
checking for PANGO... yes

checking for PANGO... yes

-------------------------------------------------------------
checking for PNG... yes

-------------------------------------------------------------
checking for RAW_R... no

-------------------------------------------------------------
checking for TIFF...
checking tiff.h usability... yes
checking tiff.h presence... yes
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checking tiffio.h usability... yes
checking tiffio.h presence... yes
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checking for TIFFOpen in -ltiff... yes
checking for TIFFClientOpen in -ltiff... yes
checking for TIFFIsByteSwapped in -ltiff... yes
checking for TIFFReadRGBATile in -ltiff... yes
checking for TIFFReadRGBAStrip in -ltiff... yes
checking if TIFF package is complete... yes
checking tiffconf.h usability... yes
checking tiffconf.h presence... yes
checking for tiffconf.h... yes
checking for TIFFIsCODECConfigured... yes
checking for TIFFMergeFieldInfo... yes
checking for TIFFIsBigEndian... yes
checking for TIFFReadEXIFDirectory... yes
checking for TIFFSetErrorHandlerExt... yes
checking for TIFFSetTagExtender... yes
checking for TIFFSetWarningHandlerExt... yes
checking for TIFFSwabArrayOfTriples... yes
-------------------------------------------------------------
checking for WEBP... no
checking for WEBPMUX... no

checking for WMF support ...
checking for libwmf/ipa.h... no
checking if WMF package is complete ... no
-------------------------------------------------------------
checking for XML... yes

-------------------------------------------------------------
checking for ImageMagick delegate programs...
checking for bpgdec... bpgdec
checking for bpgenc... bpgenc
checking for blender... blender
checking for xdg-open... /usr/bin/xdg-open
checking for ufraw-batch... ufraw-batch
checking for soffice... /usr/bin/soffice
checking for dvips... /usr/bin/dvips
checking for magick... magick
checking for magick... magick
checking for xterm... /usr/bin/xterm
checking for dot... /usr/bin/dot
checking for hp2xx... hp2xx
checking for html2ps... html2ps
checking for ilbmtoppm... /usr/bin/ilbmtoppm
checking for ppmtoilbm... /usr/bin/ppmtoilbm
checking for JxrDecApp... JxrDecApp
checking for JxrEncApp... JxrEncApp
checking for lepton... lepton
checking for lp... /usr/bin/lp
checking for lpr... /usr/bin/lpr
checking for gimp... /usr/bin/gimp
checking for magick... magick
checking for avconv... avconv
checking for ffmpeg... (cached) avconv
checking for avconv... avconv
checking for ffmpeg... (cached) avconv
checking for mrsidgeodecode... mrsidgeodecode
checking for mv... /bin/mv
checking for pcl6... pcl6
checking for gsx... no
checking for gsc... no
checking for gs... /usr/bin/gs
checking for rm... /bin/rm
checking for rsvg-convert... rsvg-convert
checking for inkscape... inkscape
checking for uniconvertor... uniconvertor
checking for dwebp... dwebp
checking for cwebp... cwebp
checking for curl... /usr/bin/curl
checking for gxps... gxps
checking for Apple fonts directory... not found!
checking for Dejavu fonts directory... not found!
checking for Ghostscript fonts directory... /usr/share/fonts/type1/gsfonts/
checking for URW-base35 fonts directory... not found!
checking for Windows fonts directory... not found!
checking for gnutar... no
checking for gtar... no
checking for tar... tar
checking for perl... perl
checking for rpmbuild... no
checking for rpm... no
checking for 7za... 7za
checking for zip... zip
-------------------------------------------------------------
checking for Ghostscript...
checking for Ghostscript version... 9.18
checking for gs color device... pnmraw
checking for gs alpha device... pngalpha
checking for gs CMYK device... pamcmyk32
checking for gs mono device... pbmraw
checking for gs PDF writing device... pdfwrite
checking for gs PS writing device... ps2write
checking for gs EPS writing device... eps2write
-------------------------------------------------------------
Update ImageMagick configuration
checking that generated files are newer than configure... done
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating common.shi
config.status: creating config/configure.xml
config.status: creating config/delegates.xml
config.status: creating config/ImageMagick.rdf
config.status: creating config/MagickCore.dox
config.status: creating config/MagickWand.dox
config.status: creating config/Magick++.dox
config.status: creating config/type-apple.xml
config.status: creating config/type-dejavu.xml
config.status: creating config/type-ghostscript.xml
config.status: creating config/type-urw-base35.xml
config.status: creating config/type-windows.xml
config.status: creating config/type.xml
config.status: creating ImageMagick.spec
config.status: creating Magick++/bin/Magick++-config
config.status: creating MagickCore/ImageMagick.pc
config.status: creating Magick++/lib/Magick++.pc
config.status: creating MagickCore/MagickCore-config
config.status: creating MagickCore/MagickCore.pc
config.status: creating MagickCore/version.h
config.status: creating Makefile
config.status: creating magick.sh
config.status: creating PerlMagick/check.sh
config.status: creating PerlMagick/default/Magick.pm
config.status: creating PerlMagick/Makefile.PL
config.status: creating PerlMagick/default/Makefile.PL
config.status: creating PerlMagick/quantum/Makefile.PL
config.status: creating PerlMagick/quantum/quantum.pm
config.status: creating PerlMagick/quantum/quantum.xs
config.status: creating PerlMagick/quantum/typemap
config.status: creating utilities/animate.1
config.status: creating utilities/compare.1
config.status: creating utilities/composite.1
config.status: creating utilities/conjure.1
config.status: creating utilities/convert.1
config.status: creating utilities/display.1
config.status: creating utilities/identify.1
config.status: creating utilities/ImageMagick.1
config.status: creating utilities/import.1
config.status: creating utilities/magick.1
config.status: creating utilities/magick-script.1
config.status: creating utilities/mogrify.1
config.status: creating utilities/montage.1
config.status: creating utilities/stream.1
config.status: creating MagickWand/MagickWand-config
config.status: creating MagickWand/MagickWand.pc
config.status: creating config/config.h
config.status: executing MagickCore/magick-baseconfig.h commands
config.status: creating MagickCore/magick-baseconfig.h - prefix MAGICKCORE for config/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
config.status: executing magick.sh.in commands
config.status: executing MagickCore-config.in commands
config.status: executing MagickWand-config.in commands
config.status: executing Magick++-config.in commands
config.status: executing PerlMagick/check.sh.in commands
configure:
==============================================================================
ImageMagick is configured as follows. Please verify that this configuration
matches your expectations.

Host system type: x86_64-pc-linux-gnu
Build system type: x86_64-pc-linux-gnu

Option Value
------------------------------------------------------------------------------
Shared libraries --enable-shared=yes yes
Static libraries --enable-static=yes yes
Build utilities --with-utilities=yes yes

 

/usr/bin/install -c -m 644 ./www/api/MagickCore/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
mkdir -p -- /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/annotated.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/classes.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/dir_101f7ac0a894e32543a314e85b2e1524.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/dirs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/doxygen.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/doxygen.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/files.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2blank.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2doc.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2folderclosed.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2folderopen.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2lastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2link.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2mlastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2mnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2node.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2plastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2pnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2vertline.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/functions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/functions_vars.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x61.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x62.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x63.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x64.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x65.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x67.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x69.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6d.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6e.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6f.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x70.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x71.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x72.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x73.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x74.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x75.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x77.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x78.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_defs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_enum.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_eval.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x63.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x64.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x67.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x69.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x6d.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x6e.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x70.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x72.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x73.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_type.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_vars.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/index.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick__wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/MagickWand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick__wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/MagickWand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/main.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__CompositeOptions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawingWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawVTable.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__MagickWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelIterator.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_b.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wandtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/bin/mkdir -p '/usr/local/share/doc/ImageMagick-7'
/usr/bin/install -c -m 644 LICENSE ChangeLog NEWS.txt '/usr/local/share/doc/ImageMagick-7'
/bin/mkdir -p '/usr/local/include/ImageMagick-7/Magick++'
/usr/bin/install -c -m 644 Magick++/lib/Magick++/Blob.h Magick++/lib/Magick++/CoderInfo.h Magick++/lib/Magick++/Color.h Magick++/lib/Magick++/Drawable.h Magick++/lib/Magick++/Exception.h Magick++/lib/Magick++/Functions.h Magick++/lib/Magick++/Geometry.h Magick++/lib/Magick++/Image.h Magick++/lib/Magick++/Include.h Magick++/lib/Magick++/Montage.h Magick++/lib/Magick++/Pixels.h Magick++/lib/Magick++/ResourceLimits.h Magick++/lib/Magick++/SecurityPolicy.h Magick++/lib/Magick++/Statistic.h Magick++/lib/Magick++/STL.h Magick++/lib/Magick++/TypeMetric.h '/usr/local/include/ImageMagick-7/Magick++'
/bin/mkdir -p '/usr/local/include/ImageMagick-7'
/usr/bin/install -c -m 644 Magick++/lib/Magick++.h '/usr/local/include/ImageMagick-7'
/bin/mkdir -p '/usr/local/share/man/man1'
/usr/bin/install -c -m 644 MagickCore/MagickCore-config.1 MagickWand/MagickWand-config.1 Magick++/bin/Magick++-config.1 utilities/ImageMagick.1 utilities/animate.1 utilities/compare.1 utilities/composite.1 utilities/conjure.1 utilities/convert.1 utilities/display.1 utilities/identify.1 utilities/import.1 utilities/magick.1 utilities/magick-script.1 utilities/mogrify.1 utilities/montage.1 utilities/stream.1 '/usr/local/share/man/man1'
/bin/mkdir -p '/usr/local/lib/pkgconfig'
/usr/bin/install -c -m 644 MagickCore/ImageMagick.pc MagickCore/MagickCore.pc MagickCore/ImageMagick-7.Q16HDRI.pc MagickCore/MagickCore-7.Q16HDRI.pc MagickWand/MagickWand.pc MagickWand/MagickWand-7.Q16HDRI.pc Magick++/lib/Magick++.pc Magick++/lib/Magick++-7.Q16HDRI.pc '/usr/local/lib/pkgconfig'
make[2]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
make[1]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] []

]]> Jit https://bioinformaticsonline.com/bookmarks/view/26252/recombination-detection-tool Tue, 02 Feb 2016 10:11:14 -0600 https://bioinformaticsonline.com/bookmarks/view/26252/recombination-detection-tool <![CDATA[Recombination detection tool]]> A program to detect recombination hotspots using population genetic data.

More at https://github.com/auton1/LDhot

Address of the bookmark: https://github.com/auton1/LDhot

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27099/rasttk-algorithm-for-building-custom-annotation-pipelines-and-annotating-batches-of-genomes Wed, 27 Apr 2016 11:07:59 -0500 https://bioinformaticsonline.com/bookmarks/view/27099/rasttk-algorithm-for-building-custom-annotation-pipelines-and-annotating-batches-of-genomes <![CDATA[RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes]]> The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/

]]> Abhi