Commit 4ca93d1a authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.9.0+dfsg

parent f9830f55

.gitignore

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@@ -21,3 +21,4 @@ 
/.cproject

/.project

/.pydevproject

tmp.kfg
 
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CHANGES.md

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# NCBI External Developer Release:





## SRA Toolkit 2.9.0

**February 23, 2018**



  **bam-load**: an issue with accessing WGS accessions was fixed  

  **bam-load**: bam-load will generate an error and quit when too many spots have been encountered  

  **bam-load**: renamed an internal function to avoid a name conflict  

  **bam-load, fastq-load**: updated to use better thread termination signaling  

  **bam-load, sra-stat**: Updated sra-stat to extract statistics of alterations made by loaders for inclusion in its report  

  **build**: Created a script that allows to add a new volume to existing repository  

  **build**: Fixed configure allowing to run it on Perl with version >= v5.26 that has "." removed from @INC  

  **build**: added "smoke tests"  

  **build**: recognize version of libhdf5 that does not allow static linking and do not try to use it  

  **build, doc**: added wiki page: Building-from-source-:--configure-options-explained  

  **build, ncbi-vdb, sra-tools**: the installation script now saves configuration files if they were modified by the user  

  **build, sra-tools**: "make runtests" now invokes "make all"  

  **build, vdb-sql**: modified build to avoid vdb-sql in absence of libxml2  

  **fastq-dump**: minor change to help text  

  **fastq-dump, vdb**: Fixed crashing of fastq-dump when dumping multiple runs with -split-3 option specified  

  **fastq-load**: preserves spot names when the platform is Illumina  

  **kfg**: added searching of configuration files in ../etc/ncbi/ relative to the binaries  

  **kfg, prefetch**: set limit of Aspera usage to 450m  

  **kfg, prefetch, remote-fuser, vfs**: Updated resolving of cache location of non-accession objects  

  **klib**: Reverted KTimeMakeTime to use UTC  

  **kns**: Accept the same http_proxy specifications as wget  

  **kns**: Added possibility to report server's IP address after network error  

  **kns**: Ignore HTTP headers sent multiple times  

  **kns**: Improved reporting of network errors  

  **kns**: fixed generation of invalid error code in response to dropped connection  

  **latf-load**: now processing multi-line sequences and qualities  

  **latf-load**: pacbio spot names with a range are now processed correctly  

  **pileup-stats**: pileup-stats now exits with code 3 if called without arguments  

  **prefetch**: fixed a bug in prefech when it printed invalid error messages after failure of reading from server  

  **sra-search**: added option --fasta for output in FASTA format  

  **sra-search**: added option to display version number  

  **sra-search**: added option to search unaligned and partially aligned fragments only  

  **sra-search**: improved performance in reference-driven mode  

  **sra-search**: various efficiency/readability improvements in the code   

  **sra-sort**: Created a separate version  of sra-sort for Complete Genomics  

  **sra-sort**: Fixed race condition in sra-sort when result was not completed when using fast drives  

  **sra-stat**: Added calculation of N50, L50, N90, L90 statistics  

  **sra-stat**: Fixed: sra-stat prints the path of alignment reference when the path is remote (http)  

  **sra-stat**: Improved performance when calculating bases statistics  

  **sra-stat**: The maximum number of reads that can be processed was Increased to 4K.  

  **sra-tools, vdb**: access to vdb/ngs via SQLite  

  **srapath**: srapath allows to get results of name resolver CGI  

  **vdb-config**: vdb-config does not fail when /repository/user/default-path is not set in configuration  

  **vdb-validate**: added a check of sum(READ_LEN) against length(READ)  

  **vfs**: Name resolving service was updated and switched to protocol version 3.0  





## SRA Toolkit 2.8.2

**March 6, 2017**
@@ -191,5 +241,3 @@ 
  **var-expand**: a tool for batch variation expansion  

  **vdb-config**: now handles standard options such as --option-file  

  **vdb-validate**: Added code to continue with the next row when column has discontiguous blobs

build/Makefile.env

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@@ -366,7 +366,7 @@ LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) 
# MallocScribble=1 is for catching allocation problems on Mac

#

ifeq ($(RUNTESTS_OVERRIDE),)

runtests: std $(TEST_TOOLS)

runtests: all $(TEST_TOOLS)

	@ export VDB_CONFIG=$(VDB_CONFIG);export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;export MallocScribble=1;\

	for i in $(TEST_TOOLS);\

	do\
@@ -384,7 +384,7 @@ endif 
# $(SLOWTESTSDATADIR) should be used to create temporary test files

SLOWTESTSDATADIR ?= /panfs/pan1.be-md.ncbi.nlm.nih.gov/sra-test/slowtests/$(shell whoami)



slowtests: std $(SLOW_TEST_TOOLS)

slowtests: all $(SLOW_TEST_TOOLS)

	@ export LD_LIBRARY_PATH=$(LIBDIR):$$LD_LIBRARY_PATH;\

	for i in $(SLOW_TEST_TOOLS);\

	do\

build/Makefile.install

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@@ -44,6 +44,18 @@ endif 
#fake root for debugging

#uncomment this line and change the test for root ( see under install: ) to succeed:

#ROOT = ~/root

ifeq (linux, $(OS))

    ifeq (0, $(shell id -u))

        LINUX_ROOT = true

    endif

endif



ifeq (true, $(LINUX_ROOT))

    KONFIG_DIR = $(ROOT)/etc/ncbi

    PROFILE_FILE = $(ROOT)/etc/profile.d/ncbi-vdb

else

    KONFIG_DIR = $(INST_BINDIR)/ncbi

endif



EXE_TARGET = $(INST_BINDIR)

PROFILE_FILE = $(ROOT)/etc/profile.d/sra-tools
@@ -62,31 +74,17 @@ $(TOOLS_TO_INSTALL): 
      $(COPY) $(BINDIR)/$@$(EXEX) $(BINDIR)/$@$(VERSION_EXEX) $(BINDIR)/$@$(MAJVERS_EXEX) $(INST_BINDIR) && \

      echo "done"



ifeq (linux, $(OS))

    ifeq (0, $(shell id -u))

        LINUX_ROOT = true

    endif

endif

copykfg:

	@ echo "Installing configuration files to $(KONFIG_DIR)"

	@ $(TOP)/build/install-kfg.sh default.kfg   $(BINDIR)/ncbi          $(KONFIG_DIR) $(TOP)/shared/kfgsums

	@ $(TOP)/build/install-kfg.sh certs.kfg     $(BINDIR)/ncbi          $(KONFIG_DIR) $(TOP)/shared/kfgsums

	@ $(TOP)/build/install-kfg.sh vdb-copy.kfg  $(TOP)/tools/vdb-copy   $(KONFIG_DIR) $(TOP)/shared/kfgsums

	@ # rename obsolete ncbi-vdb.kfg

	@ if [ -f $(KONFIG_DIR)/ncbi-vdb.kfg ] ; \

        then mv -v $(KONFIG_DIR)/ncbi-vdb.kfg  $(KONFIG_DIR)/ncbi-vdb.kfg.orig  ; fi



install: installexes

install: installexes copykfg

ifeq (true, $(LINUX_ROOT))

	@ # install configuration file(s)

	@ printf "Installing configuration files to $(ROOT)/etc/ncbi/..."

	( mkdir -p $(ROOT)/etc/ncbi && \

	  cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(ROOT)/etc/ncbi ; \

	  if [ -f $(BINDIR)/ncbi/default.kfg ] ; then \

	    if [ -f $(ROOT)/etc/ncbi/default.kfg ] ; then \

          mv -v $(ROOT)/etc/ncbi/default.kfg $(ROOT)/etc/ncbi/default.kfg.orig;\

	    fi; \

	    cp -p $(BINDIR)/ncbi/default.kfg $(ROOT)/etc/ncbi ; \

	  fi; \

	  if [ -f $(BINDIR)/ncbi/certs.kfg ] ; then \

	    if [ -f $(ROOT)/etc/ncbi/certs.kfg ] ; then \

          mv -v $(ROOT)/etc/ncbi/certs.kfg $(ROOT)/etc/ncbi/certs.kfg.orig; \

	    fi; \

	    cp -p $(BINDIR)/ncbi/certs.kfg $(ROOT)/etc/ncbi ; \

	  fi ) && echo done

	@ #

	@ echo "Updating $(PROFILE_FILE).[c]sh"

	@ printf \

"#version $(VERSION)\n"\
@@ -100,25 +98,6 @@ ifeq (true, $(LINUX_ROOT)) 
"if ( \$$status ) setenv PATH $(EXE_TARGET):\$$PATH\n"\

        >$(PROFILE_FILE).csh && chmod 644 $(PROFILE_FILE).csh || true;

	@ #TODO: check version of the files above

else    

	@ # install configuration file(s)

	@ printf "Installing configuration files to $(INST_BINDIR)/ncbi/..."

	( mkdir -p $(INST_BINDIR)/ncbi && \

	  cp -p $(TOP)/tools/vdb-copy/vdb-copy.kfg $(INST_BINDIR)/ncbi/ ; \

	  if [ -f $(BINDIR)/ncbi/default.kfg ] ; then \

	    if [ -f $(INST_BINDIR)/ncbi/default.kfg ] ; then \

          mv -v $(INST_BINDIR)/ncbi/default.kfg \

                $(INST_BINDIR)/ncbi/default.kfg.orig; \

	    fi; \

	    cp -p $(BINDIR)/ncbi/default.kfg $(INST_BINDIR)/ncbi ; \

	  fi; \

	  if [ -f $(BINDIR)/ncbi/certs.kfg ] ; then \

	    if [ -f $(INST_BINDIR)/ncbi/certs.kfg ] ; then \

          mv -v $(INST_BINDIR)/ncbi/certs.kfg \

                $(INST_BINDIR)/ncbi/certs.kfg.orig; \

	    fi; \

	    cp -p $(BINDIR)/ncbi/certs.kfg $(INST_BINDIR)/ncbi ; \

	  fi ) && echo done

endif



#-------------------------------------------------------------------------------

build/Makefile.vers

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# ===========================================================================



# SRA-TOOLS and library version

VERSION = 2.8.2
 
VERSION = 2.9.0