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

Install latest Perl (with supporting multithreading) and CPANMinus.

 $ cd
 $ git clone git://github.com/tokuhirom/plenv.git ~/.plenv
 $ git clone git://github.com/tokuhirom/Perl-Build.git ~/.plenv/plugins/perl-build/
 $ echo 'export PATH="$HOME/.plenv/bin:$PATH"' >> ~/.bashrc
 $ echo 'eval "$(plenv init -)"' >> ~/.bashrc
 $ source ~/.bashrc
 $ plenv install 5.18.1 -Dusethreads
 $ plenv rehash
 $ plenv global 5.18.1
 $ plenv install-cpanm

• git is a distributed revision control and source code management software which can help you to download files from GitHub server.
• echo means "print".
• >> means adding the output into the end of the file, while > means adding the output by overwriting the whole file. Please use> with additional cares.
• In Linux system, there are two types of outputs when you execute a command. One is called standard output (or sometimes STDOUT for short), and the other is a standard error (STDERR). 1> is for STDOUT only, 2> is for STDERR only, and &>means for both. In default > is the same to 1>.
• exec is execution.
• Remember to install Perl in supporting multithreading (with option -Dusethreads), which is important for many NGS analysis packages (e.g. Trinity). In this setting, you can use multiple CPU for Perl software.
• Install the CPAN (Comprehensive Perl Archive Network) manager software, CPANMinus, by install-cpanm.

You can use plenv global and plenv local to change the different version of Perl to fulfil different needs of your Perl software.

For example, if the specific version of Perl is not compatible with your script, you can switch to the different version by:

 $ plenv local 

• It is similar to set the local version of your script language when you use pyenv and rbenv as the following.

Put the following path into ~/.bashrc file.

export PERL5LIB="$HOME/.plenv/build/perl-5.18.1/lib"

Install BioPerl and PerlIO::gzip

CPANMinus is a very good Perl module manager, use cpanm to install BioPerl can save you a lot of time. Here are some useful modules:

$ cpanm Bio::Perl
$ cpanm Bio::SearchIO
$ cpanm PerlIO::gzip

For more information, please visit: https://github.com/tokuhirom/plenv

'du' – Check the size of a directory

$ du
This command ( du) gives you a list of directories that exist in the current working directory along with their sizes in kilobytes (default). The last line of the output gives you the total size of the current directory including its subdirectories.

$ du /home/jin1
The above command would give you the directory size of the directory /home/david

$ du -h
The same “du”command with some flag gives you a better output than the default one. The option '-h' stands for human readable format. Therefore, in order to print the sizes of the files / directories in your desire notation use this time suffixed with a 'k' if its kilobytes and 'M' if its Megabytes and 'G' if its Gigabytes.

$ du -ah
If you are interested in checking everything present in a folder use above mentioned command. It gives us not only the directories but also all the files that are present in the current directory. The “-a” flag displays the filenames along with the directory names in the output.

$ du -c
This gives you a grand total as the last line of the output. So if your directory occupies 30MB the last 2 lines of the output would be 30M.

$ du -s
Use this command to displays a summary of the directory size. It is the simplest way to know the total size of the current directory.

$ du -S
This would display the size of the current directory excluding the size of the subdirectories that exist within that directory. So it basically shows you the total size of all the files that exist in the current directory.

$ du --exculde=mp3
Several times it required to exclude some directory in our size calculation. In such cases the above command would display the size of the current directory along with all its subdirectories, but it would exclude all the files having the given pattern present in their filenames.

'df' - finding the disk free space / disk usage

$ df
Hmmm … now “df” command is really useful, and I guess you are going to use it over time. Typing the above command, outputs a table consisting of 6 columns. All the columns are very easy to understand. Remember that the 'Size', 'Used' and 'Avail' columns use kilobytes as the unit. The 'Use%' column shows the usage as a percentage which is also very useful.

$ df -h
Displays the same output as the previous command but the '-h' indicates human readable format. Hence instead of kilobytes as the unit the output would have 'M' for Megabytes and 'G' for Gigabytes.

Example: Linux installed on /dev/hda1
$ df -h | grep /dev/hda1

All right, this is not the only option to check the sizes and free spaces but there are a few more options that can be used with 'du' and 'df' . I will discuss it later.

Main features of YASS are:

• multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off
• transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T])
• using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies
• parameterizable output filter for low complexity repeats
• reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion)
• post-processing step to group gapped alignments

Address of the bookmark: http://bioinfo.lifl.fr/yass/

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments:

• FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints.
• FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy.
• FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above.
• The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned (see the picture and movie at the top of the page).

You can see more information on the FAQ. 

Address of the bookmark: http://fsa.sourceforge.net/

The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

Address of the bookmark: http://www.bx.psu.edu/~ratan/

The most used mappers of DNA-seq data are BWA and Bowtie for DNA-Seq data and Tophat, STAR or HISAT for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).

Address of the bookmark: http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data

This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

Address of the bookmark: https://github.com/fenderglass/maf2synteny