tde-users April 2013

users@trinitydesktop.org

28 participants
25 discussions

by William Morder

Hello all, I've been watching the conversations on your Trinity users lists with great interest, but haven't had much time to participate myself. (I am not really a lurker, just busy!) Over the past couple years I keep trying to upgrade my system, especially after the Ubuntu family released 12.04 LTS. I got TDE to run pretty well on top of Ubuntu, Kubuntu and Lubuntu, with varying degrees of success. It seems to run best on Lubuntu for some reason, perhaps because it is less cluttered with possibly conflicting software. When I get frustrated, I go back to go old Hardy Heron 8.04.2, which still runs best on my system; however, I am determined to stick with an up-to-date system, sooner or later, for obvious reasons. Hardy gets less and less functional with every passing day. But I like how it runs (or ran), with all my personal modifications. So I much appreciate all the hard work of the developers. I've read most of your discussions, trying to keep up with problems and fixes, and almost feel like I know some of you personally. Right now I'm running Trinity on top of Lubuntu 12.04 Precise, and it is stable and fast, and I've managed to fix a few problems myself, like windows that crash in Konqueror or Nautilus, etc. A couple things I really miss from my Hardy system, though: kshowmail and TorK. I like kshowmail, but any good email checker, which just shows headers, senders, etc. would be just as good. However, I have tried various biff-type programs, and they don't even seem to run. There are a couple others that look promising, but which either don't run at all, or at any rate don't run on Trinity. If somebody could create Trinity packages for kshowmail and TorK, I would be glad to give up my left arm, as I don't use it much anyway. TorK is the one that I really miss. Vidalia just doesn't cut it for me, and TorK had some special features that I miss. I looked through the packages and dependencies, and it seems like most or all of the dependencies are already part of Trinity. By the way, I did do a little research into alternative solutions. I tried enabling Maverick repositories, as suggested on one site, but it doesn't work. I tried downloading archived packages from various sources, then installing with gdebi-kde, etc.; that sometimes appears to work, but when I run TorK, nothing happens. I tried converting Slackware packages to .deb files using alien, but these also do not actually install. I tried compiling from source, and again, it seems to work, but only creates folders, and my system says that it is a virtual program. Any ideas, and I would be glad to try them, as I seem to have run out of other options. At present, building my own packages for TorK and dependencies is beyond my skill level. Thanks for any help, Bill Morder

11 years, 11 months

change default text editor

by Mag. Dr. Nikolaus Klepp

Hi all! Is there a way to change the default text editor? I would like to use kwrite instead of kate. I'm running 3.5.13-2 from Slavec's repository. Nik

11 years, 11 months

A Memory Comparison of Light Linux Desktops

by Slávek Banko

Hello everyone, you might also be interested in: http://l3net.wordpress.com/2013/03/17/a-memory-comparison-of-light-linux-de… http://l3net.wordpress.com/2013/04/09/a-memory-comparison-of-light-linux-de… It surprised me Razor-qt. I have to say that this environment is not nearly as complete and comprehensive as Trinity, but memory consumption is staggering. That would be a consequence of using Qt4? The choice to remain in Trinity with Qt3 => TQt3 seems to be a very good decision. Slavek --

11 years, 11 months

Assembly for differential expression analysis

by Jose Trejo

Dear Trinity developpers, I have been using the program to assemble the transcriptome of an organism without a good quality genome. The purpose of this transcriptome is to be used for differential expression analysis. Since I wanted the transcriptome to be as complete as possible I relied on high coverage. For my first assembly I used ~1 billion single-end reads, these reads are from different libraries and the length range goes from 25 to 75 bp. After running Trinity I got 320276 contigs longer than 100 bp. As some of the contigs were redundant I decided to used minimus2 to merge very similar sequences, and I ended up with more than 100000 contigs. When I mapped the libraries that I want to analyze for differential expression more than 89 % of the reads per library were mappable and around 1-2 % of the reads were aligning to more than one place, so I was quite happy with these results. I understand that with very high coverage I could be assembling transcripts that originated from pervasive transcription, and I think that this could be one of the reasons why I am getting over 100000 contigs, besides fragmentation. But this might not be a major problem since I could apply filters before proceeding with the differential expression analysis, for example I could only keep contigs that have more than x number of reads. However, now I have access to paired-end libraries and to other single-end libraries that have longer reads (75-100 bp), therefore I assembled these new libraries to check whether paired-end information could solve fragmentation problems. All together I had 2682537009 reads and I used in silico normalization to reduce the number of reads to 107846820. For the normalization I did not used the --PARALLEL_STATS parameter (memomy limitations). I followed the same pipeline than with my first assembly and after Trinity and minimus2 I have 200655 contigs. Nevertheless, now I have more redundant contigs, for instance some components have more than 100 sequences and they are sharing at least 50 bp; and I do not see an evident gain in completeness when I compare my two transcriptomes, at least with the assays that I carried out, such as checking the number and coverage of orthologous sequences that are included in the assemblies, using as reference the transcriptome of the phylogenetically closest organism. At this point I do not know whether it will be better to use my first assembly for further analysis or to try to assemble my new dataset again using options like --REDUCE (as previously suggested http://sourceforge.net/mailarchive/forum.php?thread_name=CAJCu8qPrOE1BjFPk%…) or --max_number_of_paths_per_node to solve redundancy problems and --min_kmer_cov to not include so lowly expressed transcripts. I would appreciate any comments or suggestions on this regard. Regards, Jose Trejo Uribe

11 years, 11 months

Filer windows

by Roel Wagenaar

After having upgraded my desktop-system from debian/squeeze to debian/wheezy, and installing trinity from the nightly-builds repository, I now find my filer windows are not showing the names under the icons. Is this a known problem? -- Roel Wagenaar, Linux-User #469851 with the Linux Counter; http://linuxcounter.net/ Antw.: Omdat het de volgorde verstoord waarin mensen tekst lezen. Vraag: Waarom is top-posting een slechte gewoonte? Antw.: Top-posting. Vraag: Wat is het meest ergerlijke in e-mail? Ignorence is when you don't know anything and somebody finds out.

11 years, 11 months

Kick-Off Launcher

by Alexandre Couture

Hi everyone! In the trinity-devel mailing list, there is a nst about keeping or removing the Kick-Off launcher. Here is a part of what is written: Timothy Pearson wrote: >> A good solution would be to 1) remove kickoff since it's unlikely that >> it is used, and doesn't keep in the style of trinity and port the cool >> features of kickoff into the original kicker panel, if there are any. > I would need a list of any improvements in Kickoff that are not in Kicker. > Copious amounts of whitespace around each widget is not considered an > improvement. ;-) Perhaps you could gather information from list members > on why they use Kickoff vs. Kicker? > Francois Andriot wrote: >Hello, I'm always using Kickoff menu instead of Kicker, so I would'nt >like it to be removed. >I currently have no problem with it. >Here are some reasons: >- I prefer having separate tabs for favorites/all >applications/Computer/History , instead of having a single huge menu >with many submenus. >- I prefer the search feature of Kickoff, which displays immediatly the >icon of the app I'm searching. In kicker, the search feature justs grays >out the directories, but I still have to browse the tree to find the >application I want. When the application list is very long, it is still >not very convenient. >- I like the way applications are shown in menu: a "big" icon, >application name written with big letters, application summary with >small letters. So there is no confusion between application name and >application summary. >Maybe we should just ship Kickoff as a separate application, like kbfx ? I have the same point of view as Francois Andriot on that and I can even add: -Kick-Off is as fast as though. If the program I want to launch is Gimp, I click on the start menu, I write ''gim'' on the keyboard and a menu with ''Gimp'' already highlighted appear. I just have to press enter. Otherwise, in the classic menu, I would have to find the ''Graphics'' menu and I would need to read all the names of every programs in the list before I can see ''Gimp'' in the list. And everybody here knows that TDE comes with plenty of programs, so depending of what you are looking for, the menu can be long... We use search engines to find what we want on the Web, but it wouldn't be a good idea on your computer? -Having a little summary of what the programs are is much more intuitive than having to start it, to see what it is. It is just more simple for users coming from Windows. -On my little Asus EEE, with a screen resolution of 800x480, the Kick-off is just the right size, where on the classic start menu, often a sub-menu takes all the screen and many columns, and it gets just confusing and harder to find what you are looking for. -I just don't get the point of users telling everywhere on this mailing list that NOTHING should change in TDE incomparison with KDE 3.5.10 and every single bit should stay identical, but the Kick-Off should be dropped. It is the same thing with Dolphin. Those are 2 KDE3 programs, it is not because they also exists in KDE4 that they are evil. If the Kick-Off is to be dropped one day or another, would it be at least possible to implement the search feature of the classic start menu in a more efficient way? Just my opinion... -Alexandre

11 years, 11 months

[trinity-users] who is ezmlm?

by David Hare

> Hi! This is the ezmlm program. I'm managing the > trinity-users(a)lists.pearsoncomputing.net mailing list. > > I'm working for my owner, who can be reached > at trinity-users-owner(a)lists.pearsoncomputing.net. > > > Messages to you from the trinity-users mailing list seem to > have been bouncing. I've attached a copy of the first bounce > message I received. > > If this message bounces too, I will send you a probe. If the probe bounces, > I will remove your address from the trinity-users mailing list, > without further notice. ?

11 years, 11 months

Re: [trinity-users] Kick-Off Launcher

by dep

said Lisi Reisz: | On Monday 15 April 2013 14:18:05 Gerhard Zintel wrote: | > If you right klick the K-Meue there is an entry "Switch to | > Kickoff Menue Style" - there you are, you can switch between the | > two styles (Classical and Kickoff) easily. Even if I might not | > use it in future I've learned from this thread that it's there | > and I'm glad about it. | | Thanks, Gerhard. | | Even this right-click does not work on my Desktop! At least, it | does work and brings things up, but nothing about other menu | styles! Since this is only of academic interest - I have no desire | to change from the default TDE style, which I like - I shan't loose | any sleep over it. ;-) This is so on your machine even when you right click the KMenu icon in Kicker? I'd never seen it before, so I looked and there it was, though I dasn't click on the choice, lest I enter the tunnel of menu doom . . . -- dep The shortest distance between you and great fingerstyle guitar playing? The new instructional DVDs from Marjorie Thompson, available now at www.MarjorieThompson.com

11 years, 11 months

PCLinuxOS TDE non-official remaster Theme switch script

by Alexandre Couture

Hi everyone! I hope everybody had an happy Easter weekend! I wrote a little Zenity script to switch between the Classic and the Modern theme on my PCLinuxOS TDE non-official remaster. It will be available in the next version of my remaster, but is also works in the current version. I have posted here the pictures of the script. I will also host the next version of my remaster on MEGA instead of FileFactory, so I won't have to split the archive and it will be easier to download! You can download the script here: http://www.filefactory.com/file/6nkm9kcgtetl/theme_switch.zip If you have any comments, drop a line! -Alexandre

11 years, 11 months

Kmail deleting quoted text

by Greg Madden

I ma using Debian Wheezy + nightly builds I am unable to delete the quoted text part of a message I am replying to. I can delete other parts of my email. Anyone else seeing this behavior? TIA -- Peace, Greg

11 years, 11 months

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tde-users April 2013