![]() Support both the old and the new versions of makeblastdb. And by adding new version of makeblastdbįor Linux 32 and 64 bit, and updating the makeblastdb command line to (-makeblastdb_folder) that allows the user to change the folder where So we fixed this by adding a new option to the SearchGUI command line Installed), and 2) the version of makeblastdb in SearchGUI was outdated. Was supported on Linux 32 bit only (unless additional libraries were Had two parts: 1) the makeblastdb Linux version included with SearchGUI Together come up with a solution that now seems to work. Just a quick update on the status of makeblastdb on Linux 64 bit.ījörn and I have been working on this over the weekend and have gfhui9jpollifm3/PeptideShaker- 0.28.1-beta.zip So please give these new versions a go and let us know how if youĪre now able to run the complete pipeline in Galaxy. The bug with the min and max charge being set to the same value has ![]() That can be used to set the folder where all the files needed during We've now added an option to the command line parameters -temp_folder Also you can have different jobs running on the same node, resulting in conflicting IO.ĭo you see any way to prevent SearchGUI and PeptideShaker to write to $HOME? Is there a way to avoid that? The reason is, that Galaxy jobs can run on cluster nodes, there you do not have write access to $HOME. Also I saw that derby is writing to $HOME. home/.compomics/gene_mappings is not allowed. All write operations in Galaxy should be done in one temporary folder. That remembers me on one thing we need to fix for full Galaxy support. If you need an example, this file is created after the first call of PathSettingsCLI. Finally, you can also set the path to the folders manually by editing the path.txt file which is located in the resources/conf folder. ![]() This option can also be used in the standard command line by appending the temp_folder flag, but doing it only once is enough. That should be the most convenient for you. You also have the option to write all files into a temporary folder using temp_folder as command line option instead of every path specifically. As soon as this will be officially released we will update the wiki on the webpages. As usual, if you run the command line without argument the possible options will be displayed. It works the same as all the other command lines options of SearchGUI and PeptideShaker. You can set the path of every temporary file created by every tool using the command line PathSettingsCLI. :)Īs a complement of information to the email of Harald here is how the new versions are working: I thought I'd include him on our development. So instead of developing the same wrappers twice, Helping out with the implementation of the Galaxy wrappers for SearchGUIĪnd PeptideShaker. He's a postdoc at Ghent University, and has showed an interest in So if you find any, please let us now.īut in any case, we should now have all we need to support SearchGUIĪnd PeptideShaker with MS-GF+ (and X!Tandem and OMSSA) in Galaxy right?įinally, note that I added a new person in the CC: Gerben Menschaert. That he can help us further improve the results.Īnd being beta versions there will probably be some bugs we haven't We are in contact with Sangtae (the MS-GF+ developer), and hope The results achieved will most likely improve in future versions. Note that our MS-GF+ support is still in development and that The complete list of parameters available use: We have not yet updated the command line wiki pages, so to see te4jpm8yqaghqzx/PeptideShaker- 0.26.3-beta.zip Once the results have been provided, they can be viewed and interpreted using a specialized application, such as PeptideShaker.We've now completed the first beta versions of SearchGUI and Note that some engines are only available on certain operating systems. Finally, you can select the search engines you would like to use and configure them independently. ![]() ![]() Pre-processing and post-processing can optionally be run. ThermoRawFileParser is built-in, which allows you to easily convert Thermo raw files into mzML or mgf.įrom the main user interface, you can load spectrum files and search settings, then set the preferred output folder. The program is Java-based, and it is available for Mac, Windows, and Linux.Īs far as input formats are concerned, the software supports mzML and mgf files as data sources. Intended to simplify the task of using several search engines at the same time via a graphical user interface, SearchGUI can also be used from the command-line, and it can be added to various analysis pipelines. It supports X! Tandem, MS Amanda, MyriMatch, MS-GF+, OMSSA, Tide, Comet, Andromeda, Novor, MetaMorpheus, and DirecTag. SearchGUI is an open-source project serving as a common interface for proteomics search and de novo engines, allowing you to configure and run multiple engines at the same time. ![]()
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