<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26629?offset=650 https://bioinformaticsonline.com/news/view/20007/roche-has-acquired-bina-technologies Tue, 30 Dec 2014 09:42:16 -0600 https://bioinformaticsonline.com/news/view/20007/roche-has-acquired-bina-technologies <![CDATA[Roche has acquired Bina Technologies !!!]]> Bina Technologies is a privately held company that provides a big data platform for centralized management and processing of next generation sequencing (NGS) data for the academic and translational research markets.  Bina will be integrated into the Roche Sequencing Unit, and will continue to focus on development of their innovative genomic analysis solution.

Roche has acquired Bina Technologies, a privately-owned biotech company based in California. The biotech’s first product was the Bina Box, a platform for secondary genomic analysis, sequence alignment, and variant calling, but since 2012, it has developed other products and platforms.

It is our shared vision with Roche that informatics and data sciences are critical elements of an end-to-end genomics solution. Fast, easy-to-use, scalable, and robust informatics solutions make a big difference in the quality and impact of the work of scientists and researchers. We believe in the future of data-driven, personalized medicine. We are passionate about accelerating that future together with Roche.

Financial details of the deal were not disclosed. For Roche, the move is yet another in a string of acquisitions. Last week (December 18), Roche paid $489 million for antibody maker Dutalys. And earlier this month, Roche bought prenatal testing company Ariosa Diagnostics.

Reference

http://blog.bina.com/news/bina-technologies-acquired-by-roche?&__hssc=109677338.1.1419953400266&__hstc=109677338.b8350f2729889b08f1325906d5236cd3.1419953400266.1419953400266.1419953400266.1&hsCtaTracking=96cac941-9372-4bbf-bacb-3ca6f1ff8cfd|3fce0f18-835b-4086-9345-388880861732

http://www.the-scientist.com/?articles.view/articleNo/41750/title/Roche-Buys-Bioinformatics-Firm/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36508/mitobim-mitochondrial-baiting-and-iterative-mapping Tue, 08 May 2018 04:15:25 -0500 https://bioinformaticsonline.com/bookmarks/view/36508/mitobim-mitochondrial-baiting-and-iterative-mapping <![CDATA[MITObim - mitochondrial baiting and iterative mapping]]> This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article can be found here. Kindly cite the article if you are using MITObim in your work. The pipeline was originally developed for Illumina data, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms.

Below you can find a few basic tutorials for how to run MITObim and I encorage you to give them a try with the testdata that comes with this Repo, just to make sure everything is running smoothly on your system. It'll only take a few minutes and will potentially safe you a lot of time down the line.

I provide further examples here as Jupyter notebooks. Get in touch if you feel like sharing your particular MITObim solution and I'd be happy to put it up here, too!

Address of the bookmark: https://github.com/chrishah/MITObim

]]> Rahul Nayak https://bioinformaticsonline.com/news/view/20331/type-hinting Fri, 09 Jan 2015 22:26:13 -0600 https://bioinformaticsonline.com/news/view/20331/type-hinting <![CDATA[Type Hinting]]> Python creator Guido van Rossum’s proposal for static type-checking annotations is inching closer to reality, and the feature has taken on a new name: type hinting.

image

Back in August, van Rossum published a proposal on the Python mailing list recommending type-checking annotations as a valuable feature for the next version of Python to improve the performance of editors and IDEs, linter capabilities, standard notation, and refactoring. Van Rossum’s latest proposal, posted late last month, outlined plans to publish a Python Enhancement Proposal (PEP) in early January to put the feature now known as type hinting on track for inclusion in Python 3.5, slated for release this September.

Reference

https://quip.com/r69HA9GhGa7J

]]> Pranjali Yadav 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/20363/postdoctoral-researcher-in-cancer-systems-biology Mon, 12 Jan 2015 01:44:11 -0600 <![CDATA[Postdoctoral Researcher in Cancer Systems Biology]]> Postdoctoral Researcher in Cancer Systems Biology
Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford
Grade 7: £30,434 - £37,394 with a discretionary range to £40,847 p.a.
Applications are invited for a Postdoctoral Researcher in Cancer Systems Biology to join a rapidly developing Bioinformatics Research Core group headed by Dr Anastasia Samsonova. The purpose of the role is to develop and deliver integrative approaches to dissect the complexity of cancer as a genomic disease. The research will focus on development and application of effective strategies for mining and integration of complex human *omics datasets and clinical/phenotypic data in cancer studies.

The role sits at the critical interface between genetics and cancer systems biology, and would suit a candidate who is interested in developing a career at the confluence of Statistics/Data Mining/Machine Learning and Biology. Ideally, you will have experience in development of analytical approaches to high-throughput and multivariate data mining and integration gained through a PhD (or equivalent) in a quantitative subject (eg mathematics, statistics, physics, engineering or computer science).

Experience of statistics and/or machine learning techniques is highly desirable as is evidence of prior experience of developing bioinformatics software and/or analysing complex *omics data sets. You will be able to work as part of a team and independently and deliver results to the required standard and schedule. You should be able to organise and prioritise your own work, as well as have excellent communication skills, both written and oral. The post will involve interactions with collaborators from such diverse fields as applied mathematics, statistics, computer science and medicine.

This is a full-time post, fixed-term until 31 March 2017. For informal enquiries, contact Dr Anastasia Samsonova (bioinformatics@oncology.ox.ac.uk).

All applicants must complete a short application form and upload a CV and supporting statement.

The closing date for applications is 12.00 noon on 26 January 2015.

More at https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form

]]> 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/20439/interactive-market-intelligence Mon, 19 Jan 2015 08:20:38 -0600 https://bioinformaticsonline.com/news/view/20439/interactive-market-intelligence <![CDATA[Interactive Market Intelligence]]> BioInformatics LLC, a premier research and advisory firm serving the life science industry, has launched groundbreaking, dynamic-data presentation platform, Interactive Market Intelligence— the only cloud-based market research analytics tool for the life science tools industry.

Superior to traditional PDF and PowerPoint reports, Interactive Market Intelligence allows end-users to filter, create and export literally thousands of views of data — all easily obtainable from a set of core metrics that include market, brand, customer and workflow analytics in well-defined segments of the life science market.

The Market for Real-Time PCR is the first in a series of topics to be explored using the Interactive Market Intelligence platform. The primary research analysis is based on a survey of 900+ international scientists performing qPCR in their laboratories.

Key data findings from "The Market for Real-Time PCR": Global market for qPCR in 2015 is estimated to be $3.6B; The average growth in qPCR throughput is expected to be at 9.8% in 2015; 22% of respondents are highly likely to switch primary suppliers of qPCR products; 50% of respondents use pre-designed primer/probe sets.

]]> Pranjali Yadav 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/opportunity/view/21537/bioinformatics-project-fellow-at-institute-of-genomics-integrative-biology-new-delhi-delhi Wed, 11 Mar 2015 03:04:38 -0500 <![CDATA[Bioinformatics Project Fellow at Institute of Genomics & Integrative Biology - New Delhi, Delhi]]> Pay Scale: Rs. 16,000/- + 30 % HRA per month
Educational Requirements: M.Sc. in Bioinformatics with at least 55% marks Qualifications: Knowledge of Perl, R and other programming language or Database management or knowledge of pipelines to analyze NGS data or experience in scientific writing and good communication skills

Details will be available at: http://www.igib.res.in/sites/default/files/26032015.pdf

No of Post: 01, 01

How To Apply: 1. Please fill up the proforma 2. Candidate cannot apply for more than two posts. Last date of receiving application is 12-03-2015. No application would be entertained with “result awaited” status or after due date. List of shortlisted candidates will be put up on CSIR-IGIB website. No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi. Note: The shortlisted candidates, have to report at 09:00 AM at Mall Road Campus, Delhi – 110007 on the day of interview along with any Photo ID card, (without photo ID card interview will not be conducted). 3 copies of updated signed C. V. (clearly mentioning Date of Birth and Hightest Qualification with percentage), Dissertation (if any), PhD thesis (if any) and original certificates/Self attested photocopies for verification.

General Instructions: Engagement is for the project and on behalf of the funding agency and the tenure shall be as mentioned above. The duration of the post is initially for One year or till the closing date of the project, whichever is earlier. Tenure may be extendable up to project duration. Contract may be terminated at any time by giving one-month notice by either side. The applicants will have no claim implicit or explicit for consideration against any CSIR/IGIB post. Candidates should note that non-fulfillment of the eligibility criterion will result in cancellation of candidature at any stage.

Last Date: 12-03-2015.
Age Limit: 28 Years

]]> 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