tde-users

users@trinitydesktop.org

21 participants
4373 discussions

SS_lib_type question
by mali salmon 04 Mar '14

04 Mar '14

Hello trinity users I used Trinity to assemble ~700M paired-end reads using the following command "Trinity.pl --seqType fq --left left.fq --right right.fq --SS_lib_type FR --output ./ --JM 300G --CPU 15" The run was successful, and I got a list of contigs. Now I realize that the data was not strand specific, and I am wondering how does the adding of "--SS_lib_type FR" parameter affect the assembly. Shall I redo the assembly? Thanks Mali

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ExeGnu asks for User + Password
by jotatb 01 Mar '14

01 Mar '14

Hi, I just installed ExeGnu on a USB stick, but KDM asks for user and password. I tried everything I could imagine, but nothing worked. Can you help, please? Thanks Jose Tadeu

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Problem with tdebase-trinity on amd64 system
by Marc Chénier 27 Feb '14

27 Feb '14

I lost my graphical desktop and now have only console access. This happened because I could not update the tdebase package with adept updater; there was always that one package left that could not be updated (something broken). So I thought I could fix this by removing the tdebase-trinity package from my system and then reinstalling the package fresh. So I rebooted and went into recovery mode to a root console and did that with apt-get remove, which also removed 2 other packages: ksmserver-trinity and tdebase-runtime-data-common-trinity Then I tried to apt-get install tdebase-trinity (and the 2 other packages) but could not do it because of an unmet dependencies problem for tdebase. About 20 packages are listed that need version pr82 and not version pr80 of tdebase. So I spent many long hours on various forums looking up info and did everything in the book: checked sources.list; did apt-get clean, autoclean, update, upgrade, dist-upgrade; tried apt-get install -f and dpkg --configure -a ; I also tried aptitude install which indicated it was going to install 3 packages but then did not because of unmet dependencies and gave me only one solution: keep the 3 packages at their current version [not installed]. I then thought of looking up the package on the TDE nightly builds website and noticed that superseded version 81 and published version 82 were marked with a red X (build failures) for amd64 systems. Is this relevant to my problem? Does that mean it will be fixed and I just have to wait a while? If not, is there a solution or a workaround so that I can get my faithful TDE desktop back? Thanks ahead for any help Marc TDE 14 (nightly builds) on Ubuntu Precise installed from live TDE-CD on an amd64 board

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[start hal in 13.04] (was: [trinity-users] does not automount usb flashdrives)
by Uwe Brauer 23 Feb '14

23 Feb '14

>> "Werner" == Werner Joss <werner(a)hoernerfranzracing.de> writes: > Am Donnerstag, 13. Februar 2014, 15:49:37 schrieb Uwe Brauer: >> This time (for Kubuntu 13.05) it works for KDE4 (so the USB >> drive and the PC are not the problem), but *not* for trinity. > might be caused by kubuntu 13.04 no longer supporting HAL, which is > what trinity 3.5.x still uses. R14 will be working without HAL, so > you probably will have to wait for that. > werner First I would like to werner for his suggestion. Indeed the hal daemon was not running on 13.04 and it took some effort to start him, basically following http://ubuntuforums.org/showthread.php?t=2140324 The crucial point was to create /etc/hal/fdi/preprobe and /etc/hal/fdi/information Then running sudo /usr/sbin/hald --daemon=yes --verbose=yes And then indeed ps aux | grep hald Returns ,---- | | 114 5761 0.6 0.0 125032 4820 ? Ssl 16:14 0:00 | /usr/sbin/hald --daemon=yes --verbose=yes | root 5762 0.0 0.0 110812 1948 ? Sl 16:14 0:00 hald-runner | root 5794 0.0 0.0 39076 1900 ? S 16:14 0:00 | hald-addon-input: Listening on /dev/input/event2 /dev/input/event0 | /dev/input/event3 /dev/input/event1 /dev/input/event7 | root 5795 0.0 0.0 39068 1820 ? S 16:14 0:00 | /usr/lib/hal/hald-addon-generic-backlight | root 5842 0.0 0.0 39072 1888 ? S 16:14 0:00 | hald-addon-storage: polling /dev/sr0 (every 2 sec) | root 5845 0.0 0.0 39084 1696 ? S 16:14 0:00 | /usr/lib/hal/hald-addon-cpufreq | 114 5846 0.0 0.0 26816 1352 ? S 16:14 0:00 | hald-addon-acpi: listening on acpid socket /var/run/acpid.socket | mjpons 5850 0.0 0.0 10648 932 pts/1 S+ 16:14 0:00 grep hal `---- which looks good, alas, I use a USB flash drive and it is *not* mounted automatically as I hoped. In Kubuntu 10.04 the ps command returns ,---- | 106 24280 0.0 0.1 16988 4564 ? Ssl 16:00 0:00 /usr/sbin/hald | root 24281 0.0 0.0 3536 1280 ? S 16:00 0:00 hald-runner | root 24310 0.0 0.0 3612 1248 ? S 16:00 0:00 hald-addon-input: Listening on /dev/input/event4 /dev/input/event7 /dev/input/event1 /dev/input/event5 /dev/input/event2 /dev/input/event0 /dev/input/event12 /dev/input/event9 /dev/input/event8 | root 24313 0.0 0.0 3612 1224 ? S 16:00 0:00 /usr/lib/hal/hald-addon-rfkill-killswitch | root 24319 0.0 0.0 3612 1236 ? S 16:00 0:00 /usr/lib/hal/hald-addon-leds | root 24326 0.0 0.0 3608 1240 ? S 16:00 0:00 /usr/lib/hal/hald-addon-generic-backlight | root 24328 0.0 0.0 3624 1252 ? S 16:00 0:00 /usr/lib/hal/hald-addon-cpufreq | 106 24329 0.0 0.0 3420 1172 ? S 16:00 0:00 hald-addon-acpi: listening on acpid socket /var/run/acpid.socket | oub 24611 0.0 0.0 3324 808 pts/3 S+ 16:05 0:00 grep hal `---- Which looks a little different. Any suggest is very very welcome Uwe Brauer

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Re: [trinity-devel] Fwd: [trinity-users] [start hal in 13.04] (was: [trinity-users] does not automount usb flashdrives)
by David C. Rankin 20 Feb '14

20 Feb '14

On 02/20/2014 11:24 AM, Werner Joss wrote: > which looks good, alas, I use a USB flash drive and it is *not* mounted > automatically as I hoped. > > In Kubuntu 10.04 the ps command returns > > ,---- > | 106 24280 0.0 0.1 16988 4564 ? Ssl 16:00 0:00 /usr/sbin/hald > | root 24281 0.0 0.0 3536 1280 ? S 16:00 0:00 hald-runner > | root 24310 0.0 0.0 3612 1248 ? S 16:00 0:00 hald-addon-input: Listening on /dev/input/event4 /dev/input/event7 /dev/input/event1 /dev/input/event5 /dev/input/event2 /dev/input/event0 /dev/input/event12 /dev/input/event9 /dev/input/event8 > | root 24313 0.0 0.0 3612 1224 ? S 16:00 0:00 /usr/lib/hal/hald-addon-rfkill-killswitch > | root 24319 0.0 0.0 3612 1236 ? S 16:00 0:00 /usr/lib/hal/hald-addon-leds > | root 24326 0.0 0.0 3608 1240 ? S 16:00 0:00 /usr/lib/hal/hald-addon-generic-backlight > | root 24328 0.0 0.0 3624 1252 ? S 16:00 0:00 /usr/lib/hal/hald-addon-cpufreq > | 106 24329 0.0 0.0 3420 1172 ? S 16:00 0:00 hald-addon-acpi: listening on acpid socket /var/run/acpid.socket > | oub 24611 0.0 0.0 3324 808 pts/3 S+ 16:05 0:00 grep hal > `---- > > Which looks a little different. > > > Any suggest is very very welcome > > Uwe Brauer First - is your install sysV or systemd? If systemd, then do you have consolekit installed? If no, then TDE must be patched to work in a systemd environment without console kit. The problem is user session/process tracking in TDE has not been updated to work with systemd. If you have systemd+consolekit and launch tdm through the old sysV init script, then everything will work through systemd compatibility mode. Without consolekit you have hit bug 1902. In that case, user mount of drives and access to sound may not work. Further, any tdeio processes opened (e.g. http/file/sftp) will not exit when the connection is closed and you will end up with LOTs of tdeio_file, tdeio_http, tdeio_sftp processes running on your box. However, there is a limit to the number of simultaneous processes that can be opened, so you will not run into a memory exhaustion situation. See: http://bugs.pearsoncomputing.net/bugzilla/show_bug.cgi?id=1902 This is a known issue and should be fixed shortly. -- David C. Rankin, J.D.,P.E.

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does not automount usb flashdrives
by Uwe Brauer 14 Feb '14

14 Feb '14

Heloo Kubuntu 13.04: using kde4 usb flash drive is found and automounted. However in trintiy automaount does not work I have to mount manually. any suggestions? thanks Uwe Brauer

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TDE depends on xorg
by Greg Madden 14 Feb '14

14 Feb '14

I have been trying to find the package or meta-package in TDE that depends (installs) the x-window system, ie xorg. Would it be a good idea to depend on xorg ,or similar, if TDE does not do so ? It is atypical ,afaikt, for most DE to not include the x-window system. Are most ou you installing TDE after installing another DE ? -- Peace, Greg

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trinity is not trinity???
by Uwe Brauer 13 Feb '14

13 Feb '14

Hi I just saw from the screenshot taken by James Downing that his control center is very different from mine (Kubuntu 10.04 or 13.04). Mine looks more that the one provided by Apple OS X. So I am puzzled: I thought: trinity is trinity? regards Uwe Brauer

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A great collection of wonderful wallpapers, which are creative-common licensed
by Alexandre 11 Feb '14

11 Feb '14

Hi! Here is a great collection of wonderful wallpapers, which are creative-common licensed: http://www.ravewallpapers.com They are a great addition for your computer, especially if you work in an office without windows to look outdoor. I found it on kde-look.org Maybe it would be a great way to refresh the collection of wallpapers released with TDE, which starts to get a little old. If someone is interested in it, I can choose some of them, so they could be part of TDE R14. Maybe a new default wallpaper could be choosen in that for the upcoming R14? Have a nice day! -Alexandre

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Trinity-DE fan blogpost
by Curt Howland 11 Feb '14

11 Feb '14

Hi. I realize that this is very much "preaching to the choir", posting this on the Trinity users list, but I thought some of you might like the post I did last night showing how easy it is to install the Trinity-DE system on Debian. http://anarchic-order.blogspot.com/ Criticisms, corrections and caveats gladly received, the comment area is open to all. What's your favorite application or feature in Trinity-DE? Mine is Kmail, by a wide margin. Curt- -- The secret of happiness is freedom, and the secret of freedom is courage. - Thucydides

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