Batch of new updates [#2/2015]

Packages list which i have recently updated on Fedora:

  • ProDy 1.6.1 (based on Python2) is released on Fedora 22/23 and EPEL6. This package is not compiled yet with Python3 because of missing dependencies on Fedora, neither packaged on EPEL7. However, i have rebuilt extra ProDy packages on a Copr project: ProDy-EPEL6.
  • Available a new rewrited Engauge-digitizer (Engauge6) that updates the older Engauge-digitizer 5; packaged for Fedora 21/22/23 but not for EPEL6/7 because of a missing needed package again (log4cpp).


  • IceCat-38.3.0 has been recently pushed on updates-testing; it updates the older IceCat-31.8.0 in Fedora 21/22/23.

[IceCat] 31.8.0 with vulnerability fixes

The packaging release #5 of IceCat-31.8.0 includes various vulnerability fixes (waiting for IceCat-38) backported from the branch 38 of Firefox.

The patches are for CVEs:



CVE-2015-4488 CVE-2015-4489




It’s strongly recommended to update your IceCat to this new rebuild:

dnf update icecat



Thanks to Mark H Weaver for his work.

[OpenMS] 2.0.0 RPMs released

OpenMS (follow this link for a quick start guide) is an openms2.0open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.

The release 2.0 is now ready to be installed from official Fedora repositories.

Please, if you’re interested, install by YUM or DNF

# dnf install openms-tools openms-tutorials openms-data openms openms-doc


For a full list of resolved issues and changed tool parameters please refer to the CHANGELOG.

OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the build system. It introduces a considerable number of new features and bug fixes.
Furthermore, we removed the dependency to GSL and replaced the functionality using Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more permissive non-GPL (e.g., Apache or BSD) license.

File formats:
– mzQuantML support (experimental)
– mzIdentML support (experimental)
– mzTab support (experimental)
– Indexed mzML support
– Support for numpress encoding in mzML
– Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)

– Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
– Improved “Tools” -> “Goto” dialog  – Improved display of m/z, RT, and intensity values 1D and 2D view

New tools:
– FeatureFinderIdentification — Detects features in MS1 data based on peptide identifications (TOPP)
– FeatureFinderMultiplex — Determination of peak ratios in LC-MS data (TOPP) for e.g. SILAC or Dimethyl labeling
– FidoAdapter — Runs the protein inference engine Fido (TOPP)
– LowMemPeakPickerHiRes — Finds mass spectrometric peaks in profile mass spectra (UTIL)
– LowMemPeakPickerHiRes_RandomAccess — Finds mass spectrometric peaks in profile mass spectra (UTIL)
– MRMTransitionGroupPicker (UTIL)
– MSGFPlusAdapter — MS/MS database search using MS-GF+ (TOPP)
– MetaboliteSpectralMatcher — Find potential HMDB ids within the given mass error window (UTIL)
– OpenSwathWorkflow — Complete workflow to run OpenSWATH (UTIL)
– PeakPickerIterative — Finds mass spectrometric peaks in profile mass spectra (UTIL)
– RTAnnotator — Annotates identification files that are missing the RT field (UTIL)
– SimpleSearchEngine — Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
– TopPerc — Facilitate input to Percolator and reintegrate (UTIL)

Deprecated tools:
– DBExporter — Exports data from an OpenMS database to a file (TOPP)
– DBImporter — Imports data to an OpenMS database (TOPP)
– FeatureFinderRaw — Determination of peak ratios in LC-MS data (TOPP)
– SILACAnalyzer — Determination of peak ratios in LC-MS data (TOPP)

Status changes:
– PhosphoScoring (UTIL -> TOPP)
Tools with major changes:
– OpenSWATH now supports MS1 extraction and labelled workflows
– OpenSWATHWorkflow single binary (high performance integrated workflow)
– IsobaricAnalyzer now supports TMT 10-plex

– Removed GSL dependencies  – Introduced low memory versions of various algorithms
– OpenMS now offers a single interface for different implementations to access mass spectrometric data
– in memory
– on disk with index
– cached on disc for fast access
as well as a chainable, low memory sequential processor of MS data (using a separate interface)
– pyOpenMS now supports python 3.x
– Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences

Third party software:
– Added Fido support
– Added MS-GF+ support

Changes to the Build System / Package System:
– Restructured repository layout and build system
– Added support for Travis CI
– Simplified pyOpenMS build system
– Support for Visual Studio 2013