tde-users

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16 participants
4446 discussions

Trinity Wheezy libr0?
by Mike Bird 29 Apr '13

29 Apr '13

tdm-trinity 4:14.0.0-0debian7+r693+pr37~wheezy from the nightly builds depends on libr0, which apt-get can't find in Wheezy. Can anyone offer a hint, or is it too soon to be testing Trinity for Wheezy? Thanks, --Mike

2 2

tde session crashing
by Greg Madden 27 Apr '13

27 Apr '13

Current Wheezy, TDE R14 I get a login screen on a boot/reboot. After entering user/passwd the session comes up then crashes. This is happening on my workstation , vm's that I test R14 with are okay, laptop install ok. The one thing that has happened to my work station is a power outage and a ups failure, powered off not shut down. Any file corruption that could cause this behavior? -- Peace, Greg

2 2

kwalletmanager not working
by Mag. Dr. Nikolaus Klepp 26 Apr '13

26 Apr '13

Hi all! I have just reinstalled Debian wheezy (64bit) + TDE (slavecs repository). The only thing I cannot get to work is kwalletmanager: - kwalletmanager is running (icon in systray). - klick on icon gives an empty window. - "new wallet" does nothing. So, any idea how I could get this thing working? I would really like to add my old wallet. Nik

2 2

Konqueror FTP issue
by Dan Youngquist 26 Apr '13

26 Apr '13

Hi all, When uploading, konqueror will send the whole file (every last byte), then sit there forever with the status window open. It does this maybe 80% of the time, and works fine the other times. Any ideas how to fix it, or should I file a bug report? This is on David Hare's Debian Wheezy respin. -- PGP key: http://homestead-products.com/pubkey.htm

1 0

request for packages - tork-trinity
by William Morder 25 Apr '13

25 Apr '13

> 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 Hi Bill, Can you please file request for packaging bug reports for both of those packages at http://bugs.trinitydesktop.org? We normally want to see links to the latest source tarball of a particular software package in a request for packaging bug as well. This process ensures that we a.) do not overlook a request and b.) that we can find the source files when the request is being worked on. Thanks! Tim Hi, Tim: The main dependency required by tork is kdelibs4c2a (along with some others that go along with it). This is already in Trinity, but doesn't work with tork, because something like tork-trinity (I presume) is needed. It seems that the tork package would also fit into these two pages, am I correct? http://bugs.trinitydesktop.org/show_bug.cgi?id=7 http://bugs.trinitydesktop.org/show_bug.cgi?id=411 There is also another page marked as resolved: http://bugs.trinitydesktop.org/show_bug.cgi?id=148 A quick search shows that there are some other packages affected by this dependency problem. I've added my comment to these pages, and also filed a bug report requesting package tork-trinity. http://bugs.pearsoncomputing.net/show_bug.cgi?id=1479 Not sure if I'm doing this right, but if not, somebody can tell me what they need. Bill (a.k.a., Enkidu)

1 0

request for packages - tork-trinity
by William Morder 25 Apr '13

25 Apr '13

1 0

request for packages
by William Morder 25 Apr '13

25 Apr '13

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

4 3

change default text editor
by Mag. Dr. Nikolaus Klepp 21 Apr '13

21 Apr '13

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

5 12

A Memory Comparison of Light Linux Desktops
by Slávek Banko 20 Apr '13

20 Apr '13

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 --

7 8

Assembly for differential expression analysis
by Jose Trejo 19 Apr '13

19 Apr '13

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

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