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- TPP:V5Feedback (11460 bytes)
25: ...tup when you log in. Could turn this into a .bat file and get rid of this problem.</s>
36: ... in "Fontconfig error: Cannot load default config file"
38: ...e a limit to post/put forms found by deleting 25+ files in petunia</s>
46: ...to unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName...
47: ...al or external command, operable program or batch file.</s> - Software:SpectraST (70083 bytes)
1: '''SpectraST''' (short for "'''Spectra''' '''S'''earch '''T'''...
3: The latest version of SpectraST is 5.0, released beta in November 2013, and offic...
17: ...g can also be several orders of magnitude faster. SpectraST can achieve a top speed of 0.001 to 0.01 second p...
25: === What's new in SpectraST 5.0 ===
38: === What's new in SpectraST 4.0 === - TPP Tutorial v1 (43187 bytes)
54: dir lists the files in a directory
60: mv moves a file to a different directory
74: lists all the .html files in the directory that start with raft4 and have ...
80: Lists all the files that start with ‘raft4041.’. Wildcards can ...
120: '''Tell your browser to save the file.''' The download is a self extracting compressed ... - Expert search and TPP usage (12929 bytes)
19: ...ld be stored in the <experiment> directory. mzXML files should be symlinked (use ln -s) to each <search_...
21: === Moving XML files ===
22: ...ou must run the following script in order for the files to work properly with the TPP:
33: # link mzXML files to current directory (like creating shortcuts)
34: foreach file ( *.mzXML ) - Building Peptide Atlas (26978 bytes)
8: ...s/pipeline/recipes/master_recipe.notes. Copy this file to <your_build>_recipe.notes, follow along, and e...
13: ===Start with one or more PeptideProphet output files (pepXML) for each experiment in each project.===
14: ...abase search engine such as SEQUEST, X!Tandem, or SpectraST, then validating the hits using PeptideProphet. I...
16: ...efreshParser is run after PeptideProphet by finishspectrastsearch. If this is not necessary -- and I don't th...
18: ... level in the directory tree. If you have to move files to achieve this, adjust the paths within them us... - TPP Tandem search (19915 bytes)
17: ...n be found at [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 sourceforge...
25: ...is software like TPP. Various proprietary and raw file format from mass spectrometer vendors can be conv...
30: ... be found at: [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 sourceforge...
61: ...family: monospace, courier">sequest.params</span> file.
63: ...se, with subdirectory IPI containing the database file <span style="color:blue;font-family: monospace, c... - Processing glycopeptide data (6720 bytes)
7: # In search results (pepXML files), change J/B back to N and also remove NXST_.
10: ...h that was done with sequest and xtandem. Xtandem params are the same as usual except that the target data...
15: useful files are in ~tfarrah/alt_nxst. Out of context, so mi...
20: ...to make it the same weight as a D) in the sequest.params, then
26: way to do this. I've outlined the files in the archive below, let me - TPP:4.4.0 Release Notes (31941 bytes)
48: * Provide path to plotspectrast.cgi when calling Lib2HTML
62: * Larger input field for filename
76: ** Add option not to generate Gaggle files
88: ...extern directory; components stored as compressed files when possible.
139: [pwiz] add a missing pwiz source file for ABI_T2D that was tripping up the xtandem buil... - ReleasePlanning (12743 bytes)
8: ...ecified in the protXML, try to see if there’s a file of the same name in the CWD, and if so use that, ...
11: * Redo Apache configuration file setup.
15: ...* Doesn't use web application conventions (single file in available-sites)
35: * Joe would love to rewrite the Make file
37: ...elected options would be saved to a simple params file of key-value pairs that would be read by a new ru... - TPP 4.5.2: Installing on Ubuntu 10.04.3 (7104 bytes)
3: ...and later please see the README and INSTALL_LINUX files found in source code distribution for instructio...
32: ...a new file <code>/usr/local/src/TPP-4.5.2/src/Makefile.config.incl</code> and populate it with
48: Copy any files from /usr/local/src/TPP-4.5.2/perl to /usr/local...
72: ...l apache about the TPP installation. Create a new file <code>/etc/apache2/sites-available/tpp-x.y.z</cod...
102: # directory for tpp's executable files - TPP:4.5.0 SVN Log (242349 bytes)
10: ..._pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx
16: ...unk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp
18: [SpectraST] Fix rare error when S/N calculation failed due t...
53: ..._pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx
54: ..._pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.h - TPP:4.6.3 SVN Log (38611 bytes)
144: [SpectraST] Different m/z tolerance for alignment and annota...
148: Moved the old sequest.params file to sequest27.params to indicate its the old
179: files. S3 sync now only available if one manually conf...
272: SpectraST: BUG not reading usernmods correctly FIXED
310: * Removed Cwd::realpath call on all S3 put of files. Problem is when - TPP Tutorial (17174 bytes)
21: ...from our [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site].
31: ...with decoys. We also include a search parameters file.
33: ...y, such as 7zip, from the web). You should find 2 files.
35: ...009_mzML_data.zip download the pre-converted mzML files] (768Mb) and unzip.
37: ...emParams.zip download the parameters and database files] (2.1Mb) and unzip. - TPP:4.7.0 SVN Log (41695 bytes)
29: [Petunia] Added utility to edit Tandem parameters files:
32: ...User is able to save parameters under a different file name
33: - No longer requiring that Tandem params filenames end in ".xml"; instead Petunia can recognize...
34: ...ed ability to list files by wildcard, not just by filename extension/ending
35: - Use a different color when choosing files vs. browsing - TPP:4.8.0 SVN Log (42174 bytes)
9: ...ng calls to extremely inefficient tpplib_perl for file extension checking; restored PPM as default unit ...
13: ...rt under Utilities; Broke out file browsing link (Files) to its own section for easy access
21: ...NSP bin link (goes to models page, with extra URL params); Added charge state to peptide link to PepXMLVie...
25: ...viz (the idea is to eventually get rid of the png file). Will require updates to schema! Also lowered ...
40: ...files and source_files_alt attributes in prot.xml files - TPP:4.8.0 Release Notes (9645 bytes)
8: ... new tool for visualizing ProteinProphet prot.xml files in the context of Gene Ontology terms
10: ** Added page for ''idconvert'' (under new ''Files'' section)
13: ** Added drop-down for quick file select; points to dbase/ and speclibs where appro...
15: ... be written in directory other than where mz[X]ML files are:
16: ...t and X!Tandem: use location of respective params file - TPP:5.0.0 SVN Log (143410 bytes)
5: structure, source files, build system, etc..
10: TPP5-Refactor: Rename all ".cxx" files as ".cpp". After a lengthy discussion
12: files in TPP.
64: ...l Visual Studio project files. These are project files
82: TPP5-Refactor: unused Win32 batch file, remove deleted directory - TPP:5.0.0 Release Notes (17167 bytes)
47: ...bmitted until completion (e.g. Copy/Paste a large file)
52: *** Added 'filter files here' hint text to files filter box
53: *** added basic Comet and Kojak params editor page
54: ...nd user info as a comment when saving comet/kojak params via Petunia
67: ...selected from account drop-down, or linked from a file - TPP 5.0.0: Installing on Ubuntu 16.04 (8525 bytes)
3: ...s of TPP, please see the README and INSTALL_LINUX files found in source code distribution for instructio...
66: Create a custom <code>site.mk</code> file with something like the following. After pasting ...
154: Next install this config file. This may vary among distributions, but this seem...
180: Extract all the example files (mzXML, tandem params, fasta database) to <code>/local/tpp/data/demo</c...
182: [STOPPED HERE. WHERE DID THESE FILES MAGICALLY COME FROM??] - TPP 5.x development: Installing on Ubuntu 16.04 (8229 bytes)
3: ...s of TPP, please see the README and INSTALL_LINUX files found in source code distribution for instructio...
57: Create a custom <code>site.mk</code> file with something like the following. After pasting ...
142: Next install this config file. This may vary among distributions, but this seem...
168: Extract all the example files (mzXML, tandem params, fasta database) to <code>/local/tpp/data/demo</c...
170: [STOPPED HERE. WHERE DID THESE FILES MAGICALLY COME FROM??]
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