<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27035?offset=1120 https://bioinformaticsonline.com/news/view/34375/the-10th-north-east-bioinformatics-network-nebinet-annual-coordinators-meet Sat, 18 Nov 2017 15:02:44 -0600 https://bioinformaticsonline.com/news/view/34375/the-10th-north-east-bioinformatics-network-nebinet-annual-coordinators-meet <![CDATA[The 10th North East Bioinformatics Network (NEBINet) Annual Coordinators' Meet]]> The 10th North East Bioinformatics Network (NEBINet) Annual Coordinators' Meet organised by the Bioinformatics Centre, St Edmund's College, Shillong and sponsored by the Department of Biotechnology, Government of India, was held at St Edmund's College Auditorium here on Thursday. Meghalaya Governor Ganga Prasad graced the inaugural programme as chief guest.
In his inaugural address, the Governor said the panorama of scientific scenario has greatly changed over the years, the thrust areas have undergone a metamorphosis but the conceptual underpinning of the basic sciences still continues.
"Of late, the activity of basic research has been intricately intertwined with technology. And we are determined to carry forward this change, for it is through technology that science can actually reach the masses in our country and afar, and the changing times have also inculcated a culture of cross-departmental and interdisciplinary research. Science and technology has always played a pivotal role in taking a nation towards greater heights by ways of innovations and inventions," he added.
Prasad also hoped that discussions, suggestions and sharing of innovative ideas during the two-day 10th NEBINet Annual Coordinators' Meet will open up new avenues to make substantial advancement in Biological Sciences which will provide a platform for proper and effective delivery mechanism for the common man.
During the inaugural function, Advisor of Department of Biotechnology Dr T Madhan Mohan gave an overview of the NEBINet and Bioinformatics programme.
President of Epygen Biotech FZ LLC, Dubai, UAE, Dr Debayan Ghosh, delivered the keynote address.
St Edmund's College governing body secretary Brother Simon Coelho and St Edmund's College Principal Dr Sylvanus Lamare also spoke during the function.

]]> 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
Get:2 http://security.ubuntu.com/ubuntu xenial-security InRelease [107 kB] 
Hit:3 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease 
Hit:4 http://be.archive.ubuntu.com/ubuntu xenial InRelease 
Get:5 http://be.archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]
Get:6 http://be.archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB] 
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]
Get:12 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [484 kB]
Get:13 http://security.ubuntu.com/ubuntu xenial-security/main i386 Packages [433 kB]
Get:14 http://security.ubuntu.com/ubuntu xenial-security/main Translation-en [209 kB]
Get:15 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [67,5 kB]
Get:16 http://security.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 Icons [68,0 kB] 
Get:17 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [107 kB]
Get:18 http://security.ubuntu.com/ubuntu xenial-security/universe DEP-11 64x64 Icons [147 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [769 kB] 
Get:20 http://be.archive.ubuntu.com/ubuntu xenial-updates/main i386 Packages [710 kB] 
Get:21 http://be.archive.ubuntu.com/ubuntu xenial-updates/main Translation-en [319 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP-11 Metadata [319 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 64x64 Icons [228 kB] 
Get:25 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 DEP-11 Metadata [246 kB]
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
Get:26 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 64x64 Icons [331 kB]
Get:27 http://be.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 DEP-11 Metadata [5.964 B]
Get:28 http://be.archive.ubuntu.com/ubuntu xenial-backports/main amd64 DEP-11 Metadata [3.328 B]
Get:29 http://be.archive.ubuntu.com/ubuntu xenial-backports/universe amd64 DEP-11 Metadata [5.088 B]
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.
Need to get 15,2 MB of archives.
After this operation, 78,5 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5core5a amd64 5.5.1+dfsg-16ubuntu7.5 [1.817 kB]
Get:2 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5dbus5 amd64 5.5.1+dfsg-16ubuntu7.5 [175 kB]
Get:3 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5network5 amd64 5.5.1+dfsg-16ubuntu7.5 [540 kB]
Get:4 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-icccm4 amd64 0.4.1-1ubuntu1 [10,4 kB]
Get:5 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-image0 amd64 0.4.0-1build1 [12,3 kB]
Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-keysyms1 amd64 0.4.0-1 [8.406 B]
Get:7 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0 amd64 1.11.1-1ubuntu1 [14,4 kB]
Get:8 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render-util0 amd64 0.3.9-1 [9.638 B]
Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xkb1 amd64 1.11.1-1ubuntu1 [29,2 kB]
Get:10 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-x11-0 amd64 0.5.0-1ubuntu2 [13,5 kB]
Get:11 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5gui5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.290 kB]
Get:12 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5widgets5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.252 kB]
Get:13 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5 amd64 5.5.1-2build1 [128 kB]
Get:14 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5-dev amd64 5.5.1-2build1 [9.724 B]
Get:15 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdrm-dev amd64 2.4.83-1~16.04.1 [229 kB]
Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-dri2-dev all 2.8-2 [12,6 kB]
Get:17 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-gl-dev all 1.4.17-1 [17,9 kB]
Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxext-dev amd64 2:1.3.3-1 [82,1 kB]
Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xf86vidmode-dev all 2.3.1-2 [6.116 B]
Get:21 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13,3 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-fixes-dev all 1:5.0-2ubuntu2 [14,2 kB]
Get:23 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxfixes-dev amd64 1:5.0.1-2 [10,9 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-damage-dev all 1:1.2.1-2 [8.286 B]
Get:25 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxdamage-dev amd64 1:1.1.4-2 [5.028 B]
Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-glx0-dev amd64 1.11.1-1ubuntu1 [26,9 kB]
Get:27 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri2-0-dev amd64 1.11.1-1ubuntu1 [8.384 B]
Get:28 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri3-dev amd64 1.11.1-1ubuntu1 [5.752 B]
Get:29 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render0-dev amd64 1.11.1-1ubuntu1 [15,3 kB]
Get:30 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0-dev amd64 1.11.1-1ubuntu1 [18,2 kB]
Get:31 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-shape0-dev amd64 1.11.1-1ubuntu1 [6.900 B]
Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xfixes0-dev amd64 1.11.1-1ubuntu1 [11,2 kB]
Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-sync-dev amd64 1.11.1-1ubuntu1 [10,1 kB]
Get:34 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-present-dev amd64 1.11.1-1ubuntu1 [6.618 B]
Get:35 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxshmfence-dev amd64 1.2-1 [3.676 B]
Get:36 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libx11-xcb-dev amd64 2:1.6.3-1ubuntu2 [9.730 B]
Get:37 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwayland-bin amd64 1.12.0-1~ubuntu16.04.3 [18,4 kB]
Get:38 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwayland-dev amd64 1.12.0-1~ubuntu16.04.3 [92,4 kB]
Get:39 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircore-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [23,7 kB]
Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf9v5 amd64 2.6.1-1.3 [326 kB]
Get:41 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf-dev amd64 2.6.1-1.3 [473 kB]
Get:42 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-dev amd64 0.5.0-1ubuntu2 [231 kB]
Get:43 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircommon-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [14,9 kB]
Get:44 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie2 amd64 0.26.3+16.04.20170605-0ubuntu1.1 [22,5 kB]
Get:45 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [5.152 B]
Get:46 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmirclient-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [42,6 kB]
Get:47 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libegl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [19,9 kB]
Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa amd64 17.2.8-0ubuntu0~16.04.1 [13,4 kB]
Get:49 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [40,2 kB]
Get:50 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 mesa-common-dev amd64 17.2.8-0ubuntu0~16.04.1 [525 kB]
Get:51 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [4.456 B]
Get:52 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1 [202 kB]
Get:53 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5concurrent5 amd64 5.5.1+dfsg-16ubuntu7.5 [24,3 kB]
Get:54 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5 amd64 5.5.1+dfsg-16ubuntu7.5 [128 kB]
Get:55 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5printsupport5 amd64 5.5.1+dfsg-16ubuntu7.5 [174 kB]
Get:56 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5 amd64 5.5.1+dfsg-16ubuntu7.5 [104 kB]
Get:57 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5test5 amd64 5.5.1+dfsg-16ubuntu7.5 [84,5 kB]
Get:58 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5xml5 amd64 5.5.1+dfsg-16ubuntu7.5 [91,8 kB]
Get:59 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qt5-qmake amd64 5.5.1+dfsg-16ubuntu7.5 [1.192 kB]
Get:60 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev-tools amd64 5.5.1+dfsg-16ubuntu7.5 [1.056 kB]
Get:61 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [931 kB]
Get:62 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [31,5 kB]
Get:63 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5-sqlite amd64 5.5.1+dfsg-16ubuntu7.5 [33,0 kB]
Get:64 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 qttranslations5-l10n all 5.5.1-2build1 [1.210 kB]
Fetched 15,2 MB in 4s (3.099 kB/s) 
Extracting templates from packages: 100%
Selecting previously unselected package libqt5core5a:amd64.
(Reading database ... 480949 files and directories currently installed.)
Preparing to unpack .../libqt5core5a_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5core5a:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5dbus5:amd64.
Preparing to unpack .../libqt5dbus5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5dbus5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5network5:amd64.
Preparing to unpack .../libqt5network5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5network5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libxcb-icccm4:amd64.
Preparing to unpack .../libxcb-icccm4_0.4.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-icccm4:amd64 (0.4.1-1ubuntu1) ...
Selecting previously unselected package libxcb-image0:amd64.
Preparing to unpack .../libxcb-image0_0.4.0-1build1_amd64.deb ...
Unpacking libxcb-image0:amd64 (0.4.0-1build1) ...
Selecting previously unselected package libxcb-keysyms1:amd64.
Preparing to unpack .../libxcb-keysyms1_0.4.0-1_amd64.deb ...
Unpacking libxcb-keysyms1:amd64 (0.4.0-1) ...
Selecting previously unselected package libxcb-randr0:amd64.
Preparing to unpack .../libxcb-randr0_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-randr0:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-render-util0:amd64.
Preparing to unpack .../libxcb-render-util0_0.3.9-1_amd64.deb ...
Unpacking libxcb-render-util0:amd64 (0.3.9-1) ...
Selecting previously unselected package libxcb-xkb1:amd64.
Preparing to unpack .../libxcb-xkb1_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-xkb1:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxkbcommon-x11-0:amd64.
Preparing to unpack .../libxkbcommon-x11-0_0.5.0-1ubuntu2_amd64.deb ...
Unpacking libxkbcommon-x11-0:amd64 (0.5.0-1ubuntu2) ...
Selecting previously unselected package libqt5gui5:amd64.
Preparing to unpack .../libqt5gui5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5gui5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5widgets5:amd64.
Preparing to unpack .../libqt5widgets5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5widgets5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5svg5:amd64.
Preparing to unpack .../libqt5svg5_5.5.1-2build1_amd64.deb ...
Unpacking libqt5svg5:amd64 (5.5.1-2build1) ...
Selecting previously unselected package libqt5svg5-dev:amd64.
Preparing to unpack .../libqt5svg5-dev_5.5.1-2build1_amd64.deb ...
Unpacking libqt5svg5-dev:amd64 (5.5.1-2build1) ...
Selecting previously unselected package libdrm-dev:amd64.
Preparing to unpack .../libdrm-dev_2.4.83-1~16.04.1_amd64.deb ...
Unpacking libdrm-dev:amd64 (2.4.83-1~16.04.1) ...
Selecting previously unselected package x11proto-dri2-dev.
Preparing to unpack .../x11proto-dri2-dev_2.8-2_all.deb ...
Unpacking x11proto-dri2-dev (2.8-2) ...
Selecting previously unselected package x11proto-gl-dev.
Preparing to unpack .../x11proto-gl-dev_1.4.17-1_all.deb ...
Unpacking x11proto-gl-dev (1.4.17-1) ...
Selecting previously unselected package x11proto-xext-dev.
Preparing to unpack .../x11proto-xext-dev_7.3.0-1_all.deb ...
Unpacking x11proto-xext-dev (7.3.0-1) ...
Selecting previously unselected package libxext-dev:amd64.
Preparing to unpack .../libxext-dev_2%3a1.3.3-1_amd64.deb ...
Unpacking libxext-dev:amd64 (2:1.3.3-1) ...
Selecting previously unselected package x11proto-xf86vidmode-dev.
Preparing to unpack .../x11proto-xf86vidmode-dev_2.3.1-2_all.deb ...
Unpacking x11proto-xf86vidmode-dev (2.3.1-2) ...
Selecting previously unselected package libxxf86vm-dev:amd64.
Preparing to unpack .../libxxf86vm-dev_1%3a1.1.4-1_amd64.deb ...
Unpacking libxxf86vm-dev:amd64 (1:1.1.4-1) ...
Selecting previously unselected package x11proto-fixes-dev.
Preparing to unpack .../x11proto-fixes-dev_1%3a5.0-2ubuntu2_all.deb ...
Unpacking x11proto-fixes-dev (1:5.0-2ubuntu2) ...
Selecting previously unselected package libxfixes-dev:amd64.
Preparing to unpack .../libxfixes-dev_1%3a5.0.1-2_amd64.deb ...
Unpacking libxfixes-dev:amd64 (1:5.0.1-2) ...
Selecting previously unselected package x11proto-damage-dev.
Preparing to unpack .../x11proto-damage-dev_1%3a1.2.1-2_all.deb ...
Unpacking x11proto-damage-dev (1:1.2.1-2) ...
Selecting previously unselected package libxdamage-dev:amd64.
Preparing to unpack .../libxdamage-dev_1%3a1.1.4-2_amd64.deb ...
Unpacking libxdamage-dev:amd64 (1:1.1.4-2) ...
Selecting previously unselected package libxcb-glx0-dev:amd64.
Preparing to unpack .../libxcb-glx0-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-glx0-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-dri2-0-dev:amd64.
Preparing to unpack .../libxcb-dri2-0-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-dri2-0-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-dri3-dev:amd64.
Preparing to unpack .../libxcb-dri3-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-dri3-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-render0-dev:amd64.
Preparing to unpack .../libxcb-render0-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-render0-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-randr0-dev:amd64.
Preparing to unpack .../libxcb-randr0-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-randr0-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-shape0-dev:amd64.
Preparing to unpack .../libxcb-shape0-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-shape0-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-xfixes0-dev:amd64.
Preparing to unpack .../libxcb-xfixes0-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-xfixes0-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-sync-dev:amd64.
Preparing to unpack .../libxcb-sync-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-sync-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxcb-present-dev:amd64.
Preparing to unpack .../libxcb-present-dev_1.11.1-1ubuntu1_amd64.deb ...
Unpacking libxcb-present-dev:amd64 (1.11.1-1ubuntu1) ...
Selecting previously unselected package libxshmfence-dev:amd64.
Preparing to unpack .../libxshmfence-dev_1.2-1_amd64.deb ...
Unpacking libxshmfence-dev:amd64 (1.2-1) ...
Selecting previously unselected package libx11-xcb-dev:amd64.
Preparing to unpack .../libx11-xcb-dev_2%3a1.6.3-1ubuntu2_amd64.deb ...
Unpacking libx11-xcb-dev:amd64 (2:1.6.3-1ubuntu2) ...
Selecting previously unselected package libwayland-bin.
Preparing to unpack .../libwayland-bin_1.12.0-1~ubuntu16.04.3_amd64.deb ...
Unpacking libwayland-bin (1.12.0-1~ubuntu16.04.3) ...
Selecting previously unselected package libwayland-dev:amd64.
Preparing to unpack .../libwayland-dev_1.12.0-1~ubuntu16.04.3_amd64.deb ...
Unpacking libwayland-dev:amd64 (1.12.0-1~ubuntu16.04.3) ...
Selecting previously unselected package libmircore-dev:amd64.
Preparing to unpack .../libmircore-dev_0.26.3+16.04.20170605-0ubuntu1.1_amd64.deb ...
Unpacking libmircore-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Selecting previously unselected package libprotobuf9v5:amd64.
Preparing to unpack .../libprotobuf9v5_2.6.1-1.3_amd64.deb ...
Unpacking libprotobuf9v5:amd64 (2.6.1-1.3) ...
Selecting previously unselected package libprotobuf-dev:amd64.
Preparing to unpack .../libprotobuf-dev_2.6.1-1.3_amd64.deb ...
Unpacking libprotobuf-dev:amd64 (2.6.1-1.3) ...
Selecting previously unselected package libxkbcommon-dev.
Preparing to unpack .../libxkbcommon-dev_0.5.0-1ubuntu2_amd64.deb ...
Unpacking libxkbcommon-dev (0.5.0-1ubuntu2) ...
Selecting previously unselected package libmircommon-dev:amd64.
Preparing to unpack .../libmircommon-dev_0.26.3+16.04.20170605-0ubuntu1.1_amd64.deb ...
Unpacking libmircommon-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Selecting previously unselected package libmircookie2:amd64.
Preparing to unpack .../libmircookie2_0.26.3+16.04.20170605-0ubuntu1.1_amd64.deb ...
Unpacking libmircookie2:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Selecting previously unselected package libmircookie-dev:amd64.
Preparing to unpack .../libmircookie-dev_0.26.3+16.04.20170605-0ubuntu1.1_amd64.deb ...
Unpacking libmircookie-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Selecting previously unselected package libmirclient-dev:amd64.
Preparing to unpack .../libmirclient-dev_0.26.3+16.04.20170605-0ubuntu1.1_amd64.deb ...
Unpacking libmirclient-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Selecting previously unselected package libegl1-mesa-dev:amd64.
Preparing to unpack .../libegl1-mesa-dev_17.2.8-0ubuntu0~16.04.1_amd64.deb ...
Unpacking libegl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Selecting previously unselected package libgles2-mesa:amd64.
Preparing to unpack .../libgles2-mesa_17.2.8-0ubuntu0~16.04.1_amd64.deb ...
Unpacking libgles2-mesa:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Selecting previously unselected package libgles2-mesa-dev:amd64.
Preparing to unpack .../libgles2-mesa-dev_17.2.8-0ubuntu0~16.04.1_amd64.deb ...
Unpacking libgles2-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Selecting previously unselected package mesa-common-dev:amd64.
Preparing to unpack .../mesa-common-dev_17.2.8-0ubuntu0~16.04.1_amd64.deb ...
Unpacking mesa-common-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Selecting previously unselected package libgl1-mesa-dev:amd64.
Preparing to unpack .../libgl1-mesa-dev_17.2.8-0ubuntu0~16.04.1_amd64.deb ...
Unpacking libgl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Selecting previously unselected package libglu1-mesa-dev:amd64.
Preparing to unpack .../libglu1-mesa-dev_9.0.0-2.1_amd64.deb ...
Unpacking libglu1-mesa-dev:amd64 (9.0.0-2.1) ...
Selecting previously unselected package libqt5concurrent5:amd64.
Preparing to unpack .../libqt5concurrent5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5concurrent5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5opengl5:amd64.
Preparing to unpack .../libqt5opengl5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5opengl5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5printsupport5:amd64.
Preparing to unpack .../libqt5printsupport5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5printsupport5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5sql5:amd64.
Preparing to unpack .../libqt5sql5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5sql5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5test5:amd64.
Preparing to unpack .../libqt5test5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5test5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5xml5:amd64.
Preparing to unpack .../libqt5xml5_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5xml5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package qt5-qmake:amd64.
Preparing to unpack .../qt5-qmake_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking qt5-qmake:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package qtbase5-dev-tools.
Preparing to unpack .../qtbase5-dev-tools_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking qtbase5-dev-tools (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package qtbase5-dev:amd64.
Preparing to unpack .../qtbase5-dev_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking qtbase5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5opengl5-dev:amd64.
Preparing to unpack .../libqt5opengl5-dev_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5opengl5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package libqt5sql5-sqlite:amd64.
Preparing to unpack .../libqt5sql5-sqlite_5.5.1+dfsg-16ubuntu7.5_amd64.deb ...
Unpacking libqt5sql5-sqlite:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Selecting previously unselected package qttranslations5-l10n.
Preparing to unpack .../qttranslations5-l10n_5.5.1-2build1_all.deb ...
Unpacking qttranslations5-l10n (5.5.1-2build1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libqt5core5a:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5dbus5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5network5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libxcb-icccm4:amd64 (0.4.1-1ubuntu1) ...
Setting up libxcb-image0:amd64 (0.4.0-1build1) ...
Setting up libxcb-keysyms1:amd64 (0.4.0-1) ...
Setting up libxcb-randr0:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-render-util0:amd64 (0.3.9-1) ...
Setting up libxcb-xkb1:amd64 (1.11.1-1ubuntu1) ...
Setting up libxkbcommon-x11-0:amd64 (0.5.0-1ubuntu2) ...
Setting up libqt5gui5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5widgets5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5svg5:amd64 (5.5.1-2build1) ...
Setting up libqt5svg5-dev:amd64 (5.5.1-2build1) ...
Setting up libdrm-dev:amd64 (2.4.83-1~16.04.1) ...
Setting up x11proto-dri2-dev (2.8-2) ...
Setting up x11proto-gl-dev (1.4.17-1) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
Setting up libxext-dev:amd64 (2:1.3.3-1) ...
Setting up x11proto-xf86vidmode-dev (2.3.1-2) ...
Setting up libxxf86vm-dev:amd64 (1:1.1.4-1) ...
Setting up x11proto-fixes-dev (1:5.0-2ubuntu2) ...
Setting up libxfixes-dev:amd64 (1:5.0.1-2) ...
Setting up x11proto-damage-dev (1:1.2.1-2) ...
Setting up libxdamage-dev:amd64 (1:1.1.4-2) ...
Setting up libxcb-glx0-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-dri2-0-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-dri3-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-render0-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-randr0-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-shape0-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-xfixes0-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-sync-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxcb-present-dev:amd64 (1.11.1-1ubuntu1) ...
Setting up libxshmfence-dev:amd64 (1.2-1) ...
Setting up libx11-xcb-dev:amd64 (2:1.6.3-1ubuntu2) ...
Setting up libwayland-bin (1.12.0-1~ubuntu16.04.3) ...
Setting up libwayland-dev:amd64 (1.12.0-1~ubuntu16.04.3) ...
Setting up libmircore-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Setting up libprotobuf9v5:amd64 (2.6.1-1.3) ...
Setting up libprotobuf-dev:amd64 (2.6.1-1.3) ...
Setting up libxkbcommon-dev (0.5.0-1ubuntu2) ...
Setting up libmircommon-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Setting up libmircookie2:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Setting up libmircookie-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Setting up libmirclient-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
Setting up libegl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Setting up libgles2-mesa:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Setting up libgles2-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Setting up mesa-common-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Setting up libgl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1) ...
Setting up libqt5concurrent5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5opengl5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5printsupport5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5sql5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5test5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5xml5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up qt5-qmake:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up qtbase5-dev-tools (5.5.1+dfsg-16ubuntu7.5) ...
Setting up qtbase5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5opengl5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up libqt5sql5-sqlite:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
Setting up qttranslations5-l10n (5.5.1-2build1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
➜ 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/blog/view/34916/bioinformatics-tools-developed-for-oxford-nanopore-data-analysis Wed, 27 Dec 2017 20:47:30 -0600 https://bioinformaticsonline.com/blog/view/34916/bioinformatics-tools-developed-for-oxford-nanopore-data-analysis <![CDATA[Bioinformatics tools developed for Oxford Nanopore data analysis !]]> MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly. Generally, assemblers are based on several different types of algorithms, such as greedy, overlap-layout-consensus (OLC), de Bruijn graph (DBG), and string graph.

List of analysis tools developed for Oxford Nanopore data

BWA
Fast nanopore data tuned alignment tool
https://github.com/lh3/bwa

GraphMap
Mapper for long and error-prone reads
https://github.com/isovic/graphmap

LAST
Nanopore tuned alignment tool
http://last.cbrc.jp/

LINKS
Software tool for long read scaffolding
https://github.com/warrenlr/LINKS/

marginAlign
Tools to align nanopore reads to a reference
https://github.com/benedictpaten/marginAlign

minoTour
Real time analysis tools
http://minotour.nottingham.ac.uk/

nanoCORR
Error-correction tool for nanopore sequence data
https://github.com/jgurtowski/nanocorr

NanoOK
Software for nanopore data, quality and error profiles
https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

Nanopolish
Nanopore analysis and genome assembly software
https://github.com/jts/nanopolish

nanopore
Variant-detection tool for nanopore sequence data
https://github.com/mitenjain/nanopore

Nanocorrect
Error-correction tool for nanopore sequence data
https://github.com/jts/nanocorrect/

npReader
Real-time conversion and analysis of nanopore reads
https://github.com/mdcao/npReader

poRe
Tool for analyzing and visualizing nanopore data
https://sourceforge.net/p/rpore/wiki/Home/

PoreSeq
Error-correction and variant-calling software
https://github.com/tszalay/poreseq

Poretools
Nanopore sequence analysis and visualization software
https://github.com/arq5x/poretools

SSPACE-LongRead
Genome scaffolding tool
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread

SMIS
Genome scaffolding tool
https://sourceforge.net/projects/phusion2/files/smis/

 

List of assemblers for Oxford Nanopore MinION long reads

LQS
DALIGNER, Celera OLC Nanocorrect,
Nanopolish corrector
https://github.com/jts/nanopolish

PBcR
HGAP or BLASR, Celera OLC
PBcR corrector
http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
–
Canu
MHAP, Celera OLC
Canu corrector
https://github.com/marbl/canu

Falcon
String graph, Celera OLC
Falcon corrector
https://github.com/PacificBiosciences/falcon

Miniasm
OLC
https://github.com/lh3/miniasm

ra-integrate
OLC
https://github.com/mariokostelac/ra-integrate/

ALLPATHS-LG
de Bruijn graph
ALLPATHS-L corrector
https://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12

SPAdes
de Bruijn graph
SPAdes corrector
http://bioinf.spbau.ru/spades

]]> biogeek https://bioinformaticsonline.com/bookmarks/view/36893/beap-blast-extension-and-assembly-program Mon, 11 Jun 2018 04:52:56 -0500 https://bioinformaticsonline.com/bookmarks/view/36893/beap-blast-extension-and-assembly-program <![CDATA[BEAP: Blast Extension and Assembly Program]]> Address of the bookmark: https://www.animalgenome.org/tools/beap/

]]> Shruti Paniwala https://bioinformaticsonline.com/researchlabs/view/35552/the-brent-lab Fri, 09 Feb 2018 10:55:27 -0600 <![CDATA[The Brent Lab]]> The Brent Lab is developing and applying computational methods for mapping gene regulation networks, modeling them quantitatively, and engineering new behaviors into them.

]]> https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus Wed, 24 Oct 2018 23:35:09 -0500 https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus <![CDATA[BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus]]> BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. 

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

]]> Jit https://bioinformaticsonline.com/pages/view/36197/bioinformatics-oneliner Tue, 10 Apr 2018 04:13:03 -0500 https://bioinformaticsonline.com/pages/view/36197/bioinformatics-oneliner <![CDATA[Bioinformatics OneLiner]]> To remove all line ends (\n) from a Unix text file:

sed ':a;N;$!ba;s/\n//g' filename.txt > newfilename_oneline.txt

To get average for a column of numbers (here the second column $2):

awk '{ sum += $2; n++ } END { if (n > 0) print sum / n; }'

To get sequence length for all sequences in a fasta file:

awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen = seqlen +length($0)}END{print seqlen}' \
filename.fasta

To copy (move, rename, etc) files based on their list in a text file:

cat file_list.txt | while read line; do cp "$line" complete_dataset/"$line"; done

To split bam files into sets with mapped and unmapped reads:

samtools view -F4 sample.bam > sample.mapped.sam
samtools view -f4 sample.bam > sample.unmapped.sam

To gzip all your fastq files using gnu parallel and gzip:

parallel gzip ::: *.fastq

To gzip all your fastq files using pigz:

pigz *.fastq

To count all sequences in a fasta file:

grep "^>" yourfile.fasta -c

To count all sequences in all fasta files in your current directory:

for a in *.fasta; do ls $a; grep "^>" -c $a; done

To keep only one copy of duplicated lines:

awk '!seen[$0]++'

To sum assembly size from SPAdes contigs.fasta or scaffolds.fasta file:

grep "^>" scaffolds.fasta | cut -f 4 -d '_' | paste -sd+ | bc

To remove everything after the first space at each line, e.g. to to simplify fasta headers:

cut -d' ' -f1 < your_file

To count reads in a all .fastq.gz files in your current folder (fast, using gnu parallel):

parallel "echo {} && gunzip -c {} | wc -l | awk '{d=\$1; print d/4;}'" ::: *.gz

To count reads in a all .fastq.gz files in your current folder:

zcat *.gz | echo $((`wc -l`/4))

To count reads in a all .fastq files in your current folder:

cat *.fastq | echo $((`wc -l`/4))

To count base pairs in a all .fastq.gz files in your current folder:

zcat *.fastq.gz | paste - - - - | cut -f 2 | tr -d '\n' | wc -c

To split multifasta file into many fasta files:

awk '/^>/ {OUT=substr($0,2) ".fa"}; {print >> OUT; close(OUT)}' Input_File

To convert Illumina FASTQ 1.3 to 1.8:

sed -e '4~4y/@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghi/!"#$%&'\''()*+,-.\/0123456789:;<=>?@ABCDEFGHIJ/' f.fastq

To convert FASTQ to FASTA:

sed -n '1~4s/^@/>/p;2~4p'

To get fastq read length distribution:

cat reads.fastq | awk '{if(NR%4==2) print length($1)}' | sort | uniq -c

To deinterleave interleaved fastq file:

cat myf.fq | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > myfile_1.fq) | cut -f 5-8 | \
tr "\t" "\n" > myf2.fq

To filter and sort contig identifiers from SPAdes assembly (e.g. here lenght >= 4000 + coverage >=100):

grep "^>" scaffolds.fasta | sed s"/_/ /"g | awk '{ if ($4 >= 4000 && $6 >= 100) print $0 }' | sort -k 4 -n | \
sed s"/ /_/"g

To append something to all headers of your fasta files:

sed 's/>.*/&YOURSTRING/' filename.fasta > new_filename.fasta

To replace/squeeze multiple adjacent spaces by only one space: 

tr -s " " < file

To filter fastq based on length (here larger than or equal to 21, but smaller than or equal to 25.

cat your.fastq | paste - - - - | awk 'length($2)  >= 21 && length($2) <= 25' | sed 's/\t/\n/g' > filtered.fastq

To print difference between the last and first row in 5th column:

awk '{if (!first){first=$5;}; last=$5;} END {print last-first}' myfile.txt

To sample only 200 first bases from all sequences in a multifasta file (e.g. from assembly scaffolds.fasta file here):

awk '/^>/{ seqlen=0; print; next; } seqlen < 200 { if (seqlen + length($0) > 200) $0 = substr($0, 1, 200-seqlen);\
 seqlen += length($0); print }' scaffolds.fasta > 200bp_scaffolds.fasta

 To pipe a compressed fasta file directly into makeblastdb.

gunzip -c fasta.gz | makeblastdb -in -

To remove sequences with duplicate fasta headers from a fasta file.

awk '/^>/{f=!d[$1];d[$1]=1}f' in.fasta > out.fasta
]]> Rahul Nayak https://bioinformaticsonline.com/pages/view/36384/binding-site-prediction-in-protein Wed, 25 Apr 2018 04:35:57 -0500 https://bioinformaticsonline.com/pages/view/36384/binding-site-prediction-in-protein <![CDATA[Binding Site Prediction in Protein !]]> The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).

Pockets Identification

CASTp

Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin

Pocket-Finder

Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.

PocketPicker

Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL
 

Binding Site Prediction

ConSurf

 
Identification of functional regions in proteins by surface-mapping of phylogenetic information
 
 
Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.  
 
Ligand Binding Sites
 
 
The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.
 
 
A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.
 

LIGSITEcsc

 
Prediction of binding site by pocket identification using the Connolly surface and degree of conservation

 
metaPocketA meta server for ligand-binding site prediction. metaPocket use LIGSITEcsc, PASS, Q-SiteFinder and SURFNET
]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

]]> BioStar https://bioinformaticsonline.com/pages/view/37590/parallel-processing-with-perl Sat, 25 Aug 2018 11:32:40 -0500 https://bioinformaticsonline.com/pages/view/37590/parallel-processing-with-perl <![CDATA[Parallel Processing with Perl !]]> Here is a small tutorial on how to make best use of multiple processors for bioinformatics analysis. One best way is using perl threads and forks. Knowing how these threads and forks work is very important before implementing them. Getting to know how these work would be really useful before reading this tutorial.

Many times in bioinformatics we need to deal with huge datasets which  are more than 100GB size. The traditional way to analysis a file is using the while loop

while (FILE){

Do something;

}

This is very slow(since we are using only one processor) and if we have 500 million lines in the dataset it takes more than a day to iterate through the whole dataset. So how do we make best use of all our processors and get the work done quickly?

Here is a very simple and efficient technique with perl which i have been using. I am  more inclined towards using perl fork than perl threads.

One of the oldest way to fork is

my $fork = fork();
if($fork){   
push (@childs,$fork); 
}
elseif($fork==0){
your code here;
exit(0);
}
else{die “Couldnt fork : $!”;}

## wait for the child process to finish
foreach(@childs){
my $tmp=waitid($_,0);
}

what a fork does is it creates a child process and takes the variables and code with it to analyze it separately (detached from the parent process) and thus a separate process is created( which usually runs on a separate processor). Thats it!! One big disadvantage of forking is its very difficult to share variables among the different processes. I will show you how to do it easily but still it has its own drawbacks.

Okie, now if you really do not want to use fork in your code, that’s okie too..There are many useful modules which do it for you very efficiently. One really useful module is Parallel::ForkManager. You can use Parallel::ForkManager to manage the number of forks you want to generate (number of processors you want to use).

Simple usage:
use Parallel::ForkManager;
my $max_processors=8;
my $fork= new Parallel::ForkManager($max_processors);
foreach (@dna) {
$fork->start and next; # do the fork
you code here;
$fork->finish; # do the exit in the child process
}
$pm->wait_all_children;

so you will be generating 8 forks which do the same thing for your each element of array. when one child finishes, Parallel::ForkManager generates a new one and thus you will be using all your processors to analyze the data. Now, if you have generated 8 child processes and want to write the data to one file. You need to lock the file to do this, because you will have problems with the buffering. You can lock the file using flock command.

open (my $QUAL, “myfile.txt”);
flock $QUAL, LOCK_EX or die “cant lock file $!”;
print $QUAL “$output”;
flock $QUAL, LOCK_UN or die “$!”;
close $QUAL;

I would not suggest using flock when dealing with multiple processes because it will decrease the processing efficiency( each child process must wait for the lock to be released by the other child process). Instead, I would suggest each fork writing to a separate file and after the processing just concatenating them.

Putting it all together, If you have 100GB data you can do this

step 1 : split the dataset equally according to number of processors you have. this may take a few hours(about 2-3 hrs for 100GB file)
You can use unix “split” command for this
for example:
my $number_split=int($number_of_entries_in_your_dataset/$max_processors);
my $split_Files=`split -l $number_split “your_file.fasta” “file_name”`;

step2: open you directory comtaining you split files and start Parallel::ForkManager.
For example:
opendir(DIRECTORY, $split_files_directory) or die $!; ### open the directory
my $fork= new Parallel::ForkManager($max_processors);
while (my $file = readdir(DIRECTORY)) { ### read the directory
if($file=~/^\./){next;}
print $file,”\n”;
########## Start fork ##########
my $pid= $super_fork->start and next;
Whatever you want to do with the split file ;
analyze my piece of $file;
######### end fork ###############
$super_fork->finish;
}
$super_fork->wait_all_children;

So basically each processor will be active with its piece of data (split file) and thus you have created 8 processes at one time which run without interfering with the other process. I again will not suggest writing output from each child process to one file(for reasons above). Write output from each fork to a separate file and finally concatenate them. Thats it, you have just increased your program speed by 8 times!! Isnt it easy?

Note:
You may worry about concatenation of the output each child generates, since it does take some time(remember 100GB). I think now you can use a mysql database LOAD DATA LOCAL INFILE command to load all the files into a single table(Should take about 3hrs for 100Gb dataset) and then export the whole table into one file. This should be faster than just concatenating them using “cat” command.(correct me if I am wrong)

Or much simpler way is to use pipes

cat output_dir/* | my_pipe or my_pipe <(file1) final_file;

Thats it guys!! Enjoy programming and please do comment. I am not a computer scientist so forgive me for any mistakes and if any please report them. Thank you.

]]> Rahul Nayak