Change log

Release History

Version Date Description
1.0 2011-03-11
1.0.1 2011-03-17
1.0.2 2011-04-15
1.0.3 2011-04-18
1.0.4 2011-04-19
1.0.5 2011-04-26
1.0.6 2011-04-28
1.0.7 2011-04-28
1.0.8 2011-05-04
1.0.9 2011-05-05
1.0.10 2011-05-05
1.0.11 2011-05-06
1.1 2012-02-05 Eoulsan 1.1 release
1.1.1 2012-04-17 Eoulsan 1.1.1 release
1.1.2 2012-05-12 Eoulsan 1.1.2 release
1.1.3 2012-05-14 Eoulsan 1.1.3 release
1.1.4 2012-05-29 Eoulsan 1.1.4 release
1.1.5 2012-06-21 Eoulsan 1.1.5 release
1.1.6 2012-06-26 Eoulsan 1.1.6 release
1.2 2013-02-23 Eoulsan 1.2 release
1.2.1 2013-03-01 Eoulsan 1.2.1 release
1.2.2 2013-03-01 Eoulsan 1.2.2 release
2.0-alpha1 2014-09-24 Eoulsan 2.0-alpha1 release
2.0-alpha2 2014-12-02 Eoulsan 2.0-alpha2 release
2.0-alpha3 2014-12-05 Eoulsan 2.0-alpha3 release
2.0-alpha4 2014-12-22 Eoulsan 2.0-alpha4 release
2.0-alpha5 2015-02-26 Eoulsan 2.0-alpha5 release
2.0-alpha6 2015-08-25 Eoulsan 2.0-alpha6 release
2.0-alpha7 2016-01-04 Eoulsan 2.0-alpha7 release
2.0-beta1 2016-03-08 Eoulsan 2.0-beta1 release
2.0-beta2 2016-03-21 Eoulsan 2.0-beta2 release
2.0-beta3 2016-04-03 Eoulsan 2.0-beta3 release
2.0-beta4 2016-04-26 Eoulsan 2.0-beta4 release
2.0-beta5 2017-04-07 Eoulsan 2.0-beta5 release
2.0 2017-11-06 Eoulsan 2.0 release

Release 1.0 – 2011-03-11

Type Changes By
Update 1.0 version. jourdren

Release 1.0.1 – 2011-03-17

Type Changes By
Update Documentation update and copyrights. jourdren
Fix In Expression computaion in local mode, remove SAM header from the list of accepted values. jourdren
Add Reads mapper can now generate SAM header from the list of the chromosomes. jourdren
Fix Keep the order the chromsomes for SAM header. jourdren
Update In filtersam step in local mode, now use picard library to read and write SAM files. jourdren
Update Remove unused packages. jourdren
Update Major Update of API: In Step, the configure() method don't need now globals parameters. The globals parameters are now the settings. jourdren
Fix In local expression computation step, now use the path of temporary directory in Settings. jourdren
Fix In expression computation, the ends of the alignments was 1 base too long. jourdren

Release 1.0.2 – 2011-04-15

Type Changes By
Update Documentation update. jourdren
Fix Fix bug in Expression computation when chromosome is not set in annotation. jourdren

Release 1.0.3 – 2011-04-18

Type Changes By
Fix Use now temporary directory defined in parameter file for genome indexing and reads mapping in local mode. jourdren

Release 1.0.4 – 2011-04-19

Type Changes By
Fix Anadiff step was not found. jourdren

Release 1.0.5 – 2011-04-26

Type Changes By
Fix Now use Bowtie read mapper with "--phred64-quals" as default argument. jourdren
Update Rename anadiff step to diffana. jourdren
Update Update documentation. jourdren

Release 1.0.6 – 2011-04-28

Type Changes By
Update In the createdesign command : Prevent adding compressed genome to design file and overwrite existing design file. Creation of the design fails if a file in the arguments does not exist. jourdren
Update Update documentation. jourdren

Release 1.0.7 – 2011-04-28

Type Changes By
Update Don't start an analysis with compressed genome or annotation in the design file. jourdren
Update Update documentation. jourdren

Release 1.0.8 – 2011-05-04

Type Changes By
Update Change the name of the keys for AWS keys in configuration file or global section of the parameter file. jourdren
Fix The path to AWS log can be omited. jourdren
Update Update documentation. jourdren

Release 1.0.9 – 2011-05-05

Type Changes By
Fix Bug in workflow when checking existing input files. jourdren
Fix Fix the number of required arguments for awsexec command. jourdren
Fix In awsexec s3:// url works now like s3n:// url. jourdren
Update Update documentation. jourdren

Release 1.0.10 – 2011-05-05

Type Changes By
Fix Don't prevent usage of compressed annotation and genome files in distributed mode. jourdren
Update Update documentation. jourdren

Release 1.0.11 – 2011-05-06

Type Changes By
Fix Only create debug files in debug mode in distributed mode. jourdren
Update Update Quickstart documentation. jourdren

Release 1.1 – 2012-02-05

Type Changes By
Fix Fix: OutOfMemoryError exception in awsmode on hadoop master node with mouse genome in _genomedescgenerator step. Fixes 7. jourdren
Fix Fix: _genericindexgenerator step fail when the name of the genome is "genome.fasta.bz2". Fixes 5. jourdren
Add Add new steps to compute alignments using gsnap and gmap. jourdren
Add Add support far all FASTQ formats. Add a new column in design file (FastqFormat) to define the FASTQ format to use. Warning default FASTQ format is now sanger. This default value can be set with phred.offset.default key. jourdren
Add The filterreads and filtersam steps are now multi-threaded in local mode. jourdren
Add Support for annotation and genome compressed files (in gzip or bzip2). jourdren
Add The createdesign command can now generate an Eoulsan design file from a Casava design file. This command can also create synbolic links for input files in the directory of the output design file. jourdren
Add Add genome mapper index storage. jourdren
Add Add genome and annotation storages and protocols (genome:// and annotation://). jourdren
Add Genome FASTA sequences can now be automatically extracted from GFF3 files. jourdren
Add Add experimental S3 multipart upload to S3DataProtocol. jourdren
Update For easier opening of the expression file with Microsoft Excel under Mac OS X, the extension of the output of the expression step is now ".tsv" and the name of the first column is renamed from "ID" to "Id". jourdren
Fix All the local steps use the temporary directory path define with the global parameter "main.tmp.dir" . jourdren
Add New framework in the the bio package to filter alignments. This framework is not currently used in filtersam step. jourdren
Add New framework in the bio package to filter reads. This framework allows plug-ins for the filterreads step. Add a new read filter based on Illumina filter flag in reads ids. jourdren
Add Support for Casava 1.8 FASTQ ids parsing. jourdren
Add The Sequence class can now handle IUPAC RNA and DNA alphabets. jourdren
Add New package for read, write and handling files generated by Illumina software (e.g. Cavasa designs, RTA logs...). jourdren
Fix Many fixes in the Worflow class. jourdren
Add Experimental support for paired-end FASTQ files in filterreads and mapreads steps (for some mappers only). jourdren
Update Update documentation and a add a tutorial about writing a step plug-in. jourdren

Release 1.1.1 – 2012-04-17

Type Changes By
Fix In distributed mode in mapping step, if temporary directory does not exist, create it. Fixes 13. jourdren
Fix Fix bug in expression computation. jourdren
Fix Fix: The number of alignment with more than one match filtered in filtersam step log is lower than the number of alignements filtered. Fixes 12. jourdren

Release 1.1.2 – 2012-05-12

Type Changes By
Fix In local mode in filter alignement step, the unique alignment written was not the unique alignment but the next alignment to proceed. Fixes 14. jourdren

Release 1.1.3 – 2012-05-14

Type Changes By
Fix The order of the parameter steps was not retained. Fixes 15. jourdren
Update In hadoop mode now for reads filter, show in reporters the count of reads that reject each filter like in local mode. jourdren

Release 1.1.4 – 2012-05-29

Type Changes By
Fix Fix out of memory in expression step in local mode with big sam files. Fixes 16. jourdren
Update Update documentation: Eoulsan application note is now publish in Bioinformatics. jourdren

Release 1.1.5 – 2012-06-21

Type Changes By
Fix Genome files created from GFF files only contains the first chromosome. Fixes 17. jourdren
Fix The _genericindexgenerator step fail when the genome was extracted from a GFF file. Fixes 18. jourdren

Release 1.1.6 – 2012-06-26

Type Changes By
Fix The create design action did not add genome:// or annotation:// file in design file if the URL contains '.' character. Fixes 19. jourdren
Fix The illuminaid filter in filterreads step reject all the reads with ids that contains index sequence with nucleotide 'N'. Fixes 20. jourdren

Release 1.2 – 2013-02-23

Type Changes By
Add Add the paired-end mode in the alignments filtering step. wallon
Add Add the mapping quality score filter in the alignments filtering step. wallon
Update Update documentation. wallon
Add The expression estimation step is now modular. wallon
Add Add the HTSeq-count program for the expression estimation step. wallon
Update Variables and shell expressions can be evaluated in the parameter file. This file can also now contains a "constants" section. jourdren
Add Add a genome description storage to speed up the startup of analysis and avoid multiple genome sequence parsing. jourdren
Update The "awsexec" command is renamed to "emrexec". jourdren
Add Eoulsan can now send mail to inform user of the end of the analysis. jourdren
Add Datatypes and dataformat can now defined in XML files. jourdren
Update Generated SAM files in Hadoop mode now contains SAM headers. jourdren
Add Differential analysis and normalization steps can be executed on an Rserve server. deshaies
Update Update the differential analysis and normalization steps with a new version of DESeq. deshaies
Add New mappers for mapping step: Bowtie2 and gsmap. jourdren
Update Remove gsnap and gmap standalone step. jourdren
Add Add a constant section in the parameter file. jourdren

Release 1.2.1 – 2013-03-01

Type Changes By
Update Add new configuration options for launching AWS EMR clusters (enabling debugging mode, EC2 key pair key to enable ssh connection to remote cluster and setting the maximal number of mapper tasks in a task tracker). jourdren
Update Enable a new locker for the reads mapping step in Hadoop mode that avoid to limit the number of maximal mapper tasks of a tasktracker to 2. jourdren
Update The default Hadoop version in AWS Elastic MapReduce mode is now 1.0.3. jourdren
Fix The order of the reads filters in parameter file is not the order the filter apply on the reads. Fixes 22. jourdren
Update In createdesign command, rename some command line option. Warning: -s is now for the path to the samplesheet and -l is for creating symbolic links. jourdren

Release 1.2.2 – 2013-03-01

Type Changes By
Fix Fix malformed sample parameter file param-local.xml jourdren

Release 2.0-alpha1 – 2014-09-24

Type Changes By
Fix In createdesign action fix the --paired-end option that was not working. jourdren
Add Add a new workflow engine to Eoulsan. Each step have now input and output ports. The user in the workflow file can now define for each step which step output port to use as source of data for an input port. The workflow engine use now data objects to represent data used by step. A data object can only contains element(s) of the same format. At the begining of a step, the worklow engine create a cartesian product between all input data to create step tasks. The tasks are then executed by a task scheduler. jourdren
Add Each step can now define if inputs are required in the working directory. If needed, a step is automaticaly added to copy required data to working directory before executing the step. jourdren
Add Each step can now define if it allow compressed data as input and can also define the compression of output data. If needed, a step is automaticaly added to uncompress data to working directory before executing the step. jourdren
Add Each step can now define if a log file must be created for the step. Each step has now a dedicated log file. jourdren
Add The "discardouput" attribute of the step tag in the workflow file allow to keep or not keep intermediate files of the worklow. jourdren
Add The format of the step result file has changed to JSON format. Add a configuration setting to also save the step result file in the old Eoulsan format. jourdren
Add Add the first parts of the code required for clusterexec action. jourdren
Add With the new workflow engine, the naming of the output files of the steps has changed. jourdren
Add Each data object contains metadata in addition to files. Add a storage for file metadata in a ".eoulsanmetadata" file in the workflow output directory. jourdren
Add Data of the workflow can be splitted in small chucks (and then merged) to achieve distributed computation on a non-hadoop cluster. jourdren
Add Use a new class called ServiceNameLoader instead of the Java standard ServiceLoader to load plugins. jourdren
Add Log are now buffered to avoid log print before the end of the parsing of the command line in exec action. jourdren
Add Add a new class EoulsanLogger dedicated to Logging. This class allow to rename the logger and usage of several log files against the thread group that call the EoulsanLogger.getLogger() method. jourdren
Add The design file and the workflow files are now copied in logs directory. jourdren
Add The log directory now contains the "working" and "task" subdirectories. jourdren
Add New Built-in variables are available in workflow file: job.id, job.uuid and logs.path. jourdren
Add Add a step dedicated to launch checker: CheckerStep. jourdren
Add The parameter file is now called workflow file. jourdren
Add Now each step write its output in a working directory. Against the workflow and Eoulsan mode, this working directory can be the local working directory (where data is removed at the end of the workflow), the Hadoop working directory (on HDFS) or the output directory. jourdren
Add The DataType concept no more exists in Eoulsan, there is now only DataFormats. jourdren
Add DataFile can now (if the protocol support it) create symbolic links, delete files, create and list directories. jourdren
Add A new locker for the reads mapping step in Hadoop mode is now used. It is based on Zookeeper and is very stable. jourdren
Add Add Eclipse code formatter policy file for Eoulsan and an additional dictionary for words used in Eoulsan code. jourdren
Add Eoulsan plugin path, JVM memory and option can be configured using environment variables. jourdren
Add Eoulsan now require Java 7. jourdren
Add Add a user interface (UI) API. This API is not stable will change in the next versions of Eoulsan. There is currently 3 available UI: "basic" (the default UI), "no" (that do nothing) and the experimental "lanterna". jourdren
Add Integration tests engine has been added to ensure Eoulsan results consistancy across versions. This integration tests can be run from maven or using the Eoulsan "it" action. To perform this tests, Eoulsan use the TestNG library. sperrin
Add Support for multiple versions of a mapper. User can now set the mapper version to use in Eoulsan workflow file. jourdren
Update The code for launching mappers and parse mappers output has been rewritten. jourdren
Update Start of porting Eoulsan Hadoop mode to Hadoop 2.x. The Eoulsan Hadoop mode currently not works. jourdren

Release 2.0-alpha2 – 2014-12-02

Type Changes By
Fix Various fixes in the workflow engine when use skipped steps. jourdren
Fix Fix createdesign bug when trying to discover the format of the input files. jourdren
Add Add a new sam2bam step. This new step currently only works in local mode. jourdren
Add Add a new step: expressionresultsannotation. This new step allow to add additional annotations to expression files and generate files in TSV, ODS or XLSX formats. jourdren
Add Add a new step: diffanaresultsannotation. This new step allow to add additional annotations to differential analysis files and generate files in TSV, ODS or XLSX formats. jourdren
Add Add a new storage protocol for additional annotations. jourdren
Update Add a new column named "AdditionalAnnotation" in the design file for the additional annotations of the genome. jourdren
Add Add a new shell step. This step allow to execute a shell command. jourdren
Update Eoulsan now use now a new instance of each step when running a step task. jourdren
Update Several updates to make Eoulsan works in an Hadoop 2.0 cluster. Work still in progress. jourdren
Update Developers can now define in Eoulsan SPI classes the classes that must not be loaded. jourdren
Update Add several enhancements to the Eoulsan integration tests engine. sperrin
Update Update of the CSS of the website, and update the main page of the website (e.g. add a screencast). jourdren
Add Add a dedicated eoulsan-docker.sh script that automatically configure Docker environment like Eoulsan resources mounts. jourdren
Add Eoulsan now use Maven 3 for building binaries and website. jourdren
Update Many clean up of Eoulsan code. Eoulsan now use the new features of Java 7. jourdren

Release 2.0-alpha3 – 2014-12-05

Type Changes By
Fix Fix Dockerfile URL to download Eoulsan. jourdren

Release 2.0-alpha4 – 2014-12-22

Type Changes By
Fix Fix HTSeq-count bug when an attribute in GFF3 file contains multiple parents. To use this fix, you must enable the "splitattributevalues" parameter in the expression step. jourdren
Fix When the identifier of a step was not equals to the step name, the step parameters where empty. jourdren
Fix Fix small issues in the workflow engine (step execution order, add an uncompression step when required, skip generators steps when only required only skipped steps). jourdren
Fix Fix many bugs in SOAP mapper wrapper. jourdren
Fix Fix some issues in the integration tests engine. sperrin
Update The create design action can now handle additional annotations. jourdren
Update The mapper step and the Eoulsan mapper API can now handle several versions and flavors (e.g. long index) of a mapper. jourdren
Update Add new binary versions for bowtie (1.1.1), bowtie2 (2.2.4), BWA (0.7.10) and GSNAP (2014-10-20). The scripts to generate this binaries has also been added to Eoulsan sources. jourdren
Add Add a new mapper: STAR 2.4.0h. A new step named "starindexgenerator" allow to create custom index for STAR (e.g. with a GFF3 file as parameter) like STAR genomeGenerate command. jourdren
Add Add new Eoulsan step for FastQC. sperrin
Add Add new Comparator class for bam file. sperrin

Release 2.0-alpha5 – 2015-02-26

Type Changes By
Fix The JSON of the result files in the job directory was not valid. jourdren
Fix Splitter and Merger steps now handle data metadata. jourdren
Fix In the SAM filter step in local mode, force to use Eoulsan temporary directory instead of the system temporary directory. jourdren
Fix If an output port of a step was not linked, all the other output ports of the step sent no token. jourdren
Fix In the STARIndexGenerator step, the GFF annotations where not uncompressed before starting the STAR indexer. jourdren
Fix In the Merger step, the data name of the merged data where not valid in some cases. jourdren
Fix In the Splitter step, a Data object was created for each file even if the file was a part of a multi-file (e.g. paired-end FASTQ files). jourdren
Fix The launch of Eoulsan "it" action failed. Add the two required dependencies in the pom.xml file (org.beanshell.bsh, v2.0b4 and com.beust.jcommander v1.12). sperrin
Fix Due to a lack of thread synchronization, in some case only a part of the list of the data to process where sent to the tasks. jourdren
Add Add an import step that allow to import files without declaring the steps that has been used to create the files. Files that are not related to the design file can be also imported using this new step. jourdren
Add Splitters and mergers now handle new formats: SAM, BAM and expression formats. jourdren
Add Add new step named "technicalreplicatemerger" that allow to merge technical replicate files of various formats (FASTQ, SAM, BAM and expression). jourdren
Add The version of a step to use can now be defined in the workflow file. jourdren
Update Many fixes and update to the IT test engine. sperrin
Update Change a command line option for the "it" action: the "-c/-conf" option has been renamed to "-testconf". sperrin
Update Add new patterns for managing comparisons between expected and tested directories: in the configuration of a test, add a pattern to check if a file exists. sperrin
Update Many fixes and update to support Hadoop 2.x. jourdren
Update If the user do not define temporary directory in the workflow file or in the Eoulsan configuration file, the default directory will be in a "tmp" directory in the job directory. jourdren
Update Remove the "-upload" option of the hadoopexec action. jourdren
Update No log file is now written on the console as now a log file is always created in the job directory. jourdren
Update Cleanup of the context object methods. jourdren
Update STAR 2.4.0j is now bundled in Eoulsan. STAR 2.4.0i has been removed. jourdren
Update BWA 0.7.12 is now bundled in Eoulsan. BWA 0.7.10 has been removed. jourdren
Update GSNAP 2014-12-21 is now bundled in Eoulsan. GSNAP 2014-10-22 has been removed. jourdren
Update The CopyInputData step now create symbolic links instead copying files if there is no necessary (un)compression is required and if the input and output files are on the same filesystem. jourdren

Release 2.0-alpha6 – 2015-08-25

Type Changes By
Fix A cartesian product was done when lanching the CopyOutputDataStep step (the step that copy the outputs of a step). jourdren
Fix CopyInputDataStep now do not uncompress input data from the design step when is not necessary. jourdren
Fix In some cases the expression computation in Hadoop mode was not correct. Several counts were missing. jourdren
Update Eoulsan code is now officialy hosted on GitHub. jourdren
Update Add a new user interface for Eoulsan based on the Lanterna library for exec and hadoopexec actions. jourdren
Update STAR 2.4.0k is now bundled in Eoulsan. STAR 2.4.0j has been removed. jourdren
Update Set "--outSAMunmapped Within" as default arguments for the STAR mapper. jourdren
Update Hadoopexec action is now working with Hadoop 2.x. Filterreads, mapreads, filtersam, filterandmap and expression steps had a dedicated implementation for Hadoop 2.x. Hadoop 1.x support in Eoulsan 2.0 has been removed. jourdren
Update The sam2bam step had now a dedicated implementation for Hadoop mode. jourdren
Update Unused mapper indexes on Hadoop cluster nodes are now automatically removed if they not been used since one week. jourdren
Update The Hadoop log is now saved in a dedicated log file in the job directory. jourdren
Update Steps without a dedicated Hadoop code can now be executed using the hadoopexec action. jourdren
Update In workflow file, the "${logs.path}" variable has been renamed to "${job.path}". jourdren
Update Eoulsan now use htsjdk 1.118 instead of samtools/picard 1.83. Samtools 1.83 is still used as runtime dependency for FastQC for reading SAM/BAM files. jourdren
Update Files with the ".gff3" extension can now also be used for GFF files. jourdren
Update The SOAP mapper and the original Eoulsan expression counter are now deprecated, they will be removed in a next version of Eoulsan. jourdren
Update The Google Errorprone static code analysis tool is now executed at each Eoulsan compilation for better source code error detection. jourdren
Update Eoulsan now produce a Graphviz file for the workflow to execute in the job directory. jourdren
Update The sam2bam step now create in local mode a symbolic link to the BAI file with the same basename than the BAM file. jourdren
Update The symbolic links created by Eoulsan in the exec action are now relative symbolic links instead of absolute symbolic links. jourdren
Update The output of all the "discardouput" steps are now removed at the end of a successful job. jourdren
Update The outputs of the failed and aborted steps are now removed. jourdren
Update Add two new read filters: "trimpolynend" and "length.minimal.length.threshold". This new filters replace the "trim.length.threshold" filter that is now deprecated and will be remove in a next version of Eoulsan. jourdren
Update Set the default compression level value in sam2bam step to 5 instead of 0. jourdren
Update The parameters "max.lines" used in many splitter steps has been renamed to "max.entries". jourdren
Update The tasks can now be launched once all the required data of the task is available. Before, tasks where launched only if all the tasks of the dependency steps where completed. jourdren
Update The genome and annotation data have now the basename of the file as name. jourdren
Add Add new step, GalaxyToolStep, it can use a Toolshed XML file from Galaxy to run new tool in Eoulsan workflow. Actually, it can be manage basic toolshed syntax. sperrin
Add Add a new FastQC step that can be launch on FASTQ or SAM files in local mode. sperrin
Add Now the FastQC step is hadoop compatible. jourdren
Update Add several enhancements to the Eoulsan integration tests report file. sperrin
Update Add a new option in the command line to override the output directory defined in the integration tests configuration. sperrin
Update Add a new IT parameter that allow to remove output files of an integration test after the end of the test to save space disk. sperrin

Release 2.0-alpha7 – 2016-01-04

Type Changes By
Fix The eoulsan.sh script now works with old bash versions. jourdren
Fix In SAM/BAM splitters and mergers, the JVM temporary directory was used instead of the Eoulsan temporary directory. jourdren
Fix In the "shell" step, if the SHELL environment variable is not set, now use /bin/sh as default shell. jourdren
Update The read mapper code has been refactored and impoved to be more efficient by using named pipes. The new code avoid copying FASTQ files on Hadoop nodes in the mapping step. Mapper binaries now can be provided by the user on the filesystem or in a Docker container. jourdren
Add Add a new action "clusterexec" that allow to execute an Eoulsan workflow on a non Hadoop cluster. HTCondor is the first cluster scheduler supported by Eoulsan in this mode. jourdren
Update Eoulsan now support the cluster scheduler of the TGCC. jourdren
Add Add a new scheduler that allow to run tasks from steps that are not designed for Hadoop on an Hadoop cluster. The steps must have the @HadoopCompatible annotation and must only the DataFile API to access to the input and output files. jourdren
Add Add "requiredprocs" and "requiredmemory" attributes for the step tag in the workflow file. This new attributes allow to define in cluster and hadoop modes the required number of processors and memory to use by a step task. jourdren
Add Add "dataproduct" atribute for the step tag in the workflow file. This new attribute allow to define the method (cross product or match) to use to combine data before executing a step. jourdren
Update Galaxytools files can now be related to a Docker image thanks to a new "dockerimage" attribute for the "command" tag of the Galaxytool files. jourdren
Update Galaxytools files can use standard interpreters (e.g. perl, python, ruby...) like with the "real" Galaxy software. jourdren
Add The createdesign action now support bcl2fastq 2 output. firmo
Update Rename "pairend.accept.pairend" read filter parameter to "pairedend.accept.paired.end" and rename "pairend.accept.signlend" read filter parameter to "pairedend.accept.single.end". jourdren
Remove The "annotationfile" parameter has been removed from expressionresultsannotation and diffanaresultsannotation steps. User must now use the AdditionalAnnotation column in the design file. jourdren
Remove The "hadoop.mapper.required.memory" parameter has been removed from the mapreads step. User must now use the "requiredmemory" attribute of the "step" tag in the workflow file to define the amount of memory required by the mapper in hadoop mode. jourdren
Update In the "expressionresultsannotation" step rename the "gtf.file" parameter to "use.gtf.file". jourdren
Remove The support for the SOAP 2 mapper has been removed. jourdren
Update The "htseq-count" count is now the default counter. jourdren
Remove Remove the old Eoulsan 1.0/1.1 expression step counter in both local and Hadoop mode. jourdren
Remove Remove all the 32 bits versions of the mappers. jourdren
Update The workfow GraphViz file now contains an example of the command to launch to create a PNG file. jourdren
Update The IlluminaReadId class now support the new Illumina FASTQ header generated by bcl2fastq 2 when no sample is indexed in a lane. jourdren
Update The "expressionresultsannotation" can now be executed on an Hadoop cluster. jourdren
Update Add new environment variable EOULSAN_JAVA_HOME that can be used to specify a JRE for Eoulsan that is not the default JRE or the JRE defined by the JAVA_HOME environment variable. jourdren
Update Now save the logs of the external libraries in a "additional.log" file in the job directory. jourdren
Add Add a "Counters" section in step result files that summaries counters of tasks with the same name (useful when using splitters and mergers in a workflow). jourdren
Update Eoulsan now check if unknown tags or attributes exists in the XML workflow file. jourdren
Update Many cleanup code, javadoc and typo fixes. jourdren
Update Add examples for all the steps. jourdren

Release 2.0-beta1 – 2016-03-08

Type Changes By
Fix At the end of an analysis that use Docker, Eoulsan now properly stop the Docker connection and had not to wait several seconds the end of the connection. jourdren
Fix Eoulsan can now execute Sweave code using R >= 3.1.0. jourdren
Fix In the "diffanaresultsannotation" step, user can now define the pattern of the files to convert and the prefix of the output files. jourdren
Fix Fix the workflows in the quickstart guide. jourdren
Fix The "diffanaresultsannotation" step now depends of the previous step in the workflow, so this step cannot be executed before the previous has finished. jourdren
Fix The standard scheduler was resumed before the end of all the tasks handled by scheduler dedicated of the steps that manage their own parallelization. jourdren
Add Add a new format for the Eoulsan design file that allow to define complex design using DESeq2. bauquet
Update Replace the implementation of the Eoulsan design object to handle the 2 formats of design files. bauquet
Add Add a new step "deseq2" that allow to perform normalization and differential analysis using DESeq2. jourdren
Add Add a new step "bam2sam" that allow to convert BAM files to SAM files. firmo
Add Add a new step "sam2fastq" that allow to convert SAM files to FASTQ files. firmo
Add Eoulsan can now handle Ctrl-C user action to properly stop a running workflow. jourdren
Update "condor" scheduler name has been renamed to "htcondor" as it is is official name since 2012. jourdren
Update Bcl2fastq samplesheet related classed are now in the Aozan dependency. jourdren
Update Reorganize translator package code. firmo
Update Rename fr.ens.transcriptome.eoulsan.* packages to fr.ens.biologie.genomique.eoulsan.* jourdren
Update The new Eouslan website URL is http://outils.genomic.biologie.ens.fr/eoulsan and the new Genomic platform website is https://genomique.biologie.ens.fr. jourdren
Update Update the links of the clickable cells in XLSX and ODS files generated by the "expressionresultsannotation" and "diffanaresultsannotation" steps. firmo
Update The URL of the links in XLSX and ODS files generated by the "expressionresultsannotation" and "diffanaresultsannotation" steps are now configurable using the main.additional.annotation.hypertext.links.path configuration parameter. jourdren
Add Now remove the uncompressed version of the genome mapper at the end of the analysis to save space. jourdren
Update Now file searching with no extension is allowed for genome://, annotation:// and additionalannotation:// protocols. jourdren
Update The search of a file is now case insensitive for genome://, annotation:// and additionalannotation:// protocols when the underlying protocols support directory listing. jourdren
Fix In STARIndexGenerator, the path to the gff file in the command line was not an absolute path like the genome file path. jourdren
Add Add new options to Normalization and diffana steps to select the R execution method (process, Rserve or Docker). Normalization and diffana steps can now work in a Docker container. jourdren
Update For normalization and differential analysis (using DESeq or DESeq2), Eoulsan now check if the required R execution method is available (R executable, Docker image or Rserve server). jourdren
Update In the "diffanaresultsannotation" and "expressionresultsannotation" steps, add an option disable the usage of an additional annotation file. jourdren
Add Add a new dataformat for the GTF files. Currently no step use this new dataformat. jourdren
Add Add a new storage protocol dedicated to GTF file: gtf://. jourdren
Update The annotation:// protocol has been renamed gff://, the annotation:// protocol is now deprecated. jourdren
Add Add the support for new job scheduler for the clusterexec mode: SLURM, TORQUE and PBS Pro. jourdren
Fix The shell and the diffanaresultsannotation now depends on all previous step and not just the previous step. jourdren
Fix In CombinedTaskScheduler, the standard scheduler was resumed before the end of all the tasks handled by the own parallelization scheduler. jourdren
Fix In the Graphviz file generated by Eoulsan at the startup of a workflow, the string are now XML escaped. jourdren
Update Reorganize Eoulsan code, many classes name related to the workflow engine has been renamed. The step package has been renamed to module, and the *Step classes to *Module. jourdren
Fix The writing module documentation page has been updated with Eoulsan 2 API. jourdren

Release 2.0-beta2 – 2016-03-21

Type Changes By
Fix In DESeq2Module, rename the "statistic.test" parameter to "statistical.test" like in Eoulsan documentation. jourdren
Fix In DESeq2 module, now correctly handle all the cases to define the references of a design. jourdren
Fix In the design format v2, the reference value of the "[Experiment]" section is now "reference" instead of "Reference" like in documentation. jourdren
Fix In the createdesign action, the "RepTechGroup" field is now created for all the experiments and not only for the default experiement. jourdren
Fix In the GFFChecker, now check sequence regions described in GFF3 files once all the GFF3 file has been parsed because the "##sequence-region" pragmas can be anywhere in the file and not only at the beginning of the file. jourdren
Fix The FastQC module can now handle input files without any entry. jourdren
Fix When using Docker, the content of the stdout and stderr files were inverted. jourdren
Fix The illuminaid read filter, do not remove now reads that not contain the Illumina filter flag. jourdren
Update When an error occurs in a workflow, the exception is now log in the Eoulsan log file. jourdren
Update Many small code and Javadoc fixes using IDEA inspect tool and Findbugs. jourdren

Release 2.0-beta3 – 2016-04-03

Type Changes By
Fix The Illumina read header parser can now parse headers from reads created using several indexes for the demultiplexing. jourdren
Update Replace homemade Cheetah interpreter implementation by the original implementation using Jython. jourdren

Release 2.0-beta4 – 2016-04-26

Type Changes By
Fix No Eoulsan class now use Spliter.splitToList() method to avoid exception when using Hadoop and its bundled version of Guava. jourdren
Fix In Eoulsan2DesignReader, The samples were not added to the experiements if no column dedicated to the experiment has been created. jourdren
Fix In the design v2, the comparisons value of the [Experiment] section is now "comparisons" like in documentation instead of "comparison". jourdren
Fix The step parameters are now evalued when parsing the <outputs> subtags in Galaxy tool files. jourdren
Fix In the DESeq2 module the comparison entries strings were not trimmed. jourdren
Update Add GTF format support in the GFFEntry class and add a GTFReader and a GTFWriter classes to read and write GTF files. jourdren
Update Add support of the GTF format for feature annotation files in the expression step. jourdren
Update Add a checker for GTF format. jourdren
Update The FastQC module can now process the two read files in paired-end. jourdren
Update Add a TMPDIR variable that contains the path to the local temporary directory when interprets the <command> tag of the Galaxy tool files. jourdren
Update In eoulsan.sh, now set the value of $TMPDIR environment variable as the JVM temporary directory if defined. jourdren
Update Add a new "main.executables.tmp.dir" configuration parameter that allow to define the temporary directory where executables are extracted from the Eoulsan jar. jourdren

Release 2.0-beta5 – 2017-04-07

Type Changes By
Fix The createdesign action can now handle GTF files. jourdren
Fix In STARIndexGeneratorModule, when a GTF file was required by user, the module still tried to open a GFF file. jourdren
Fix Fix links in XLSX files created by Eoulsan. jourdren
Fix Fix lock issue in Hadoop mode with STAR mapper. jourdren
Fix The stderr output is now redirected to /dev/null for all mappers to avoid fullil the stderr buffer by the mapper and block the mapping. jourdren
Fix Fix issues when parsing DESeq2 module parameters. jourdren
Fix Fix issues when generating plots with DESeq2. jourdren
Fix In HTSeq-count, now check if input data is paired-end by reading the data instead of using Eoulsan metadata. jourdren
Fix Fix the "diffanaresultsannotation" module to avoid saving output files on HDFS in Hadoop mode. jourdren
Fix In design step, now get the compression of the files even if storage protocols have been used (e.g. genonme:// or gff://). jourdren
Add The createdesign action can now handle several bcl2fastq samplesheets arguments. jourdren
Add Add several read filters that come from Trimmomatic. jourdren
Add Add STAR 2.5.2b binary in the Eouslan jar. This version is now the default version for Eoulsan. jourdren
Add Add GSNAP/GMAP STAR 2017-02-25 binary in Eouslan jar. jourdren
Add Add a new data type for cutadapt adapters. jourdren
Add Add new methods for the Sequence class: reverse(), complement(), reverseComplement(), getIdentifierInName() and getDescriptionInName(). jourdren
Update The output files of each step are now saved in a dedicated directory. jourdren
Update The createdesign action now use for the default condition and the technical replicate the sample name instead of the sample id. jourdren
Update Modules that require Docker can now be used in Hadoop mode. jourdren
Update The default arguments with Bowtie 2 are now: "-k 2". jourdren
Update Rename the "mapping.quality" SAM filter to "quality". jourdren
Update GMAP mapper can now be used in Eoulsan as a flavor of GSNAP. jourdren
Update For the BWA mapper, user can now use the "mem" alignment algorithm in addition of the "aln" algorithm by selecting the flavor of the mapper. jourdren
Update In expression module in local mode, add a new counter that indicate the number of missing mate alignments. jourdren

Release 2.0 – 2017-11-06

Type Changes By
Fix Fix issues with BWA mem wrapper. jourdren
Fix When using a Galaxy module in Docker mode with input files that are outside the workflow directory, they were not mounted in the container. jourdren
Fix The XLSX files created by Eoulsan now use a formula to create hyperlinks in XLSX spreadsheets. This is more portable with Microsoft Excel and Libreoffice. jourdren
Fix In clusterexec mode, the result of the task was sending to the deseriablized workflow and not to the real workflow. jourdren
Fix The name of tasks were not always as expected in the step result files. jourdren
Fix Fix NullPointerException when the required Docker images were not installed. jourdren
Fix Many fixes in the workflow engine to improve the stability of the software. jourdren
Fix The mapping stalled when FASTQ input files were empty or very small. jourdren
Add Add GMAP/GSNAP 2017-04-24 to Eoulsan. jourdren
Add Add "asap" as a new value for the "discardoutput" attribute of the workflow to remove output files of a step once all the steps that require this outputs are completed. jourdren
Add Add a new filter to select only a type of Nanopore sequence. jourdren
Add Eoulsan can now handle Galaxy tools with text parameters. jourdren
Add Add support for HTCondor ConcurrencyLimits. The defined value will be used for all submitted jobs. jourdren
Add Add a "main.docker.mount.nfs.roots" global parameter that allow to avoid some right issues with files stored on NFS storage and Docker. jourdren
Add Add a new class NanoporeReadId to easily parse Nanopore read ids. jourdren
Add Add classes to handle expression matrices. jourdren
Add Add the Fast5 class from the Toullig project in Eoulsan. jourdren
Update The generate-casava-design-validator.sh script that is now in Aozan git repository. jourdren
Update Big refactoring of the API of the readsmapper package. The new API is more convinient and easier to improve. jourdren
Update The "requiredprocs" attribute can now be use for standard steps in local mode. jourdren
Update Update HTCondor wrapper to handle last HTCondor version changes. jourdren
Update Add a "copy" parameter in the import module. This will allow to always copy files to import. jourdren
Update In "clusterexec" mode, now use a waiting queue for all scheduler status queries instead of a sleeping time for each job. Now waits one second between two queries. jourdren
Update Now use the "HH:MM:SS.mmm" format instead of the "MM:SS.mmm" format. jourdren