<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/28141?offset=1070 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/opportunity/view/18579/cluster-innovation-center-university-of-delhi Wed, 22 Oct 2014 10:39:49 -0500 <![CDATA[CLUSTER INNOVATION CENTER @ UNIVERSITY OF DELHI]]> Applications for Pre-selection of candidates under ‘Institutions Mode’ for DST-ISPIRE Faculty in Computational Biology/ Systems Biology/ Bioinformatics

Applications are invited for pre-selection of candidates for Ministry of Science and Technology, Department of Science and Technology INSPIRE Faculty Scheme: a component of “Assured Opportunity for Research Career (AORC)” under INSPIRE in the area of computational Biology/Systems Biology/Bioinformatics.

Candidates having done their B.Tech/B.E. and or M.Sc./M.Tech in Computer Science or Biotechnology and Ph.D. in Systems/ Computational Biology or Bioinformatics may apply in the following format prescribed by DST to the Director, Cluster Innovation Center, University Stadium, GC Narang Marg, University of Delhi, Delhi -11107. Detials of other qualification, age limits etc., please visit www.inspire-dst.gov.in.

Application on the prescribed format may be submitted by email to director@cic.du.ac.in before October 25, 2014. Selected candidates shall be called for an interview. The date, time and venue of the interview shall be informed by email/telephone. For more information about Cluster Innovation Center, please visit https://ducic.ac.in.

]]> https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala https://bioinformaticsonline.com/news/view/19059/ipython-interactive-notebooks Fri, 07 Nov 2014 12:07:02 -0600 https://bioinformaticsonline.com/news/view/19059/ipython-interactive-notebooks <![CDATA[IPython: Interactive notebooks]]> The IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document.

These notebooks are normal files that can be shared with colleagues, converted to other formats such as HTML or PDF, etc. You can share any publicly available notebook by using the IPython Notebook Viewer service which will render it as a static web page. This makes it easy to give your colleagues a document they can read immediately without having to install anything.

image

To learn more about using the IPython Notebook, you can visit our example collection, and you can read the documentation for all the details on how to use and configure the system. The Notebook Gallery showcases many interesting notebooks covering a variety of topics, from basic programming to advanced scientific computing.

 

More http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261

http://ipython.org/ipython-doc/1/interactive/notebook.html

Reference http://ipython.org/notebook.html

]]> Rahul Nayak https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny Mon, 06 Nov 2023 03:09:59 -0600 https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny <![CDATA[Bioinformatics Tools for Phylogeny !]]> Direct access to the individual tools available on this server.

Multiple Alignment:Phylogeny:Tree viewers:Utilities:
MUSCLE PhyML TreeDyn Gblocks
T-Coffee / 3DCoffee TNT Drawgram Jalview
ClustalW BioNJ Drawtree Readseq
ProbCons MrBayes ATV (A Tree Viewer) Built-in converter
]]> BioStar https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools Fri, 05 Jan 2018 04:02:22 -0600 https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools <![CDATA[ECTOOLS: Long Read Correction and other Correction tools]]> Long Read Correction and other Correction tools

This package is a loose collection of scripts. To run the correction
routine see the section below. Descriptions of the other scripts
are at the bottom of this file.

Contact: gurtowsk@cshl.edu

In short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read data. More background information for the algorithm can be found:
http://schatzlab.cshl.edu/presentations/2013-06-18.PBUserMeeting.pdf

Address of the bookmark: https://github.com/jgurtowski/ectools

]]> Jit https://bioinformaticsonline.com/opportunity/view/19161/niab-molecular-biologybioinformatics-scientistra-openings Thu, 13 Nov 2014 13:37:27 -0600 <![CDATA[NIAB Molecular Biology/Bioinformatics Scientist/RA Openings]]> D. No. 1-121/1, 4th and 5th Floors, Axis Clinicals Building, Miyapur, Hyderabad, Telangana, India- 500 049

Email: admin@niab.org.in Telephones: +91 40 2304 9403 Telefax: +91 40 2304 2740
Advertisement No: 5/2014

About NIAB National Institute of Animal Biotechnology (NIAB), Hyderabad, an autonomous institute under the aegis of Department of Biotechnology, Government of India, is aimed to harness novel and emerging biotechnologies and create knowledge in the cutting edge areas for improving animal health and productivity.

Applications are invited for the following temporary research positions to work in ongoing DBTBBSRC sponsored research project entitled “Transcriptome Analysis in Indian buffalo and the Genetics of Innate Immunity” at the National Institute of Animal Biotechnology, Hyderabad.

(A) Project Scientist – Level B (One Position)

Emoluments: Rs. 15600 + GP Rs. 5400 + 30 % HRA p.m. (Total emoluments will be Rs. 49,770/-p.m. for the duration of the project)

Essential Qualification: Candidates having M.V.Sc. in Veterinary Microbiology / Veterinary Pathology / Veterinary Public Health / Ph.D. degree in Life Sciences, Biotechnology, Molecular Biology or any other related field from the recognized university are eligible to apply.

The candidate should have a good academic record and research experience as evidenced from published in standard referred journals / patents.

Desirable: Candidates having research experience in the area of tissue culture, genomics, Transcriptomics and Advanced Molecular Biology will be given preference.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

(B) Research Associate in Bioinformatics (One position)

Fellowship: Rs. 22,000 + 30 % HRA

Essential Qualification: Candidates having Ph.D. degree or M.Tech. with three years of
experience in Bioinformatics, Computational Biology, Biotechnology, Life Sciences or any other related field are eligible to apply.

Desirable: Candidate having research experience in the area of next generation sequencing (NGS) data analysis, Genome wide association studies, Genomic selection, advance genomic data analysis etc., will be given preference. The candidate should have a good academic record and research experience as evidenced from published papers in standard journals / patents.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

Project Duration: The duration of the project is Three years and the positions are co- terminus with the duration of the project. (Initial appointment will be for one year and further extension will be granted based on annual review).

Mode of submission of application: Only online applications are to be submitted through
www.niab.org.in on or before 08 December, 2014. Link for online submission of applications will be available from 10 November 2014.

Advertisement: www.niab.org.in/Notifications/Advt_5_2014/Advt_5_2014.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/36516/metassembler-merging-and-optimizing-de-novo-genome-assemblies Tue, 08 May 2018 04:52:33 -0500 https://bioinformaticsonline.com/bookmarks/view/36516/metassembler-merging-and-optimizing-de-novo-genome-assemblies <![CDATA[Metassembler: merging and optimizing de novo genome assemblies]]> Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. 

Address of the bookmark: https://sourceforge.net/projects/metassembler/?source=directory

]]> Rahul Nayak https://bioinformaticsonline.com/opportunity/view/19249/bioinformatics-jrfrasrf-position-at-panjab-university Wed, 19 Nov 2014 20:19:49 -0600 <![CDATA[Bioinformatics JRF/RA/SRF position at PANJAB UNIVERSITY]]> CENTRE FOR SYSTEMS BIOLOGY & BIOINFORMATICS
UIEAST, PANJAB UNIVERSITY, CHANDIGARH

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of
the project.

Essential Qualification

For Research Fellow:-

M.Sc. in Systems Biology and Bioinformatics / Life Sciences with minimum 55% marks.

Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

For Program Assistant:-

The candidate must have M.Sc./M.Tech/MCA/PGDCA in Computer Science and must be able to handle LAN, Linex. Preference will be given to the candidate having experience in
System Administration.

Emoluments

For Research Fellow Rs. 12,500/- per month (Fixed)
For Program Assistant Rs. 12,500/- per month (Fixed)

Applications should be reach on or before 19-11-2014 in the office of the undersigned.

Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

Advertisement:

http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter Fri, 12 Oct 2018 04:37:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter <![CDATA[DNA Nucleotide Counter]]> DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

]]> Neel