Commit 0da2357f authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.10.2+dfsg

parent 40995143

CHANGES.md

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# NCBI External Developer Release:





## SRA Toolkit 2.10.2

**January 15, 2020**



  **cloud, kfg, vdb-config**: added command line options for cloud configuration  

  **fasterq-dump**: fixed bug of random error at startup  

  **kfg, kns, krypto, prefetch, vdb-config, vfs**: names service URL was updated to locate.ncbi.nlm.nih.gov  

  **kfg, prefetch, vfs**: fixed possibility to prefetch karts with genotype and phenotype files  

  **latf-load**: latf-load now preserves read names  

  **prefetch**: accepts JWT cart command line argument  

  **prefetch**: accepts JWT cart command line argument plus accession filter  

  **prefetch**: fixed crash when run with --output-file option  

  **prefetch**: make sure to accept old style kart file; added --cart command line option  

  **prefetch**: the download transport has been limited to https and the eliminate-quals option has been temporarily disabled  

  **prefetch, vfs**: allow to specify file type to resolve  

  **prefetch, vfs**: allow to use "prefetch --type all" to request download of all file types  

  **sra-pileup**: printing bases inbetween slices when user-defined ref-name given fixed  

  **sra-stat**: can accept any number of reads  

  **srapath**: fixed regression when an extra vdbcache URL is printed  

  **srapath**: fixed regression when resolving protected data  

  **sratools**: add --perm option to all accessor tools  

  **sratools**: added --ngc command line argument  

  **sratools**: fastq-dump accepts both -v and --verbose to enable verbose mode  

  **sratools**: sratools accept --ngc to specify the ngc file  

  **sratools**: sratools accepts -Z for fasterq-dump  

  **sratools**: sratools was rewritten as a stand-alone binary  

  **sratools, vdb-config**: dbGaP page removed  

  **vdb, vdb-config**: GUID shown in vdb-config or created if not yet present  

  **vdb, vdb-dump**: fixed an error reporting bug  

  **vdb-config**: allow multiple saves in interactive mode  

  **vdb-config**: disabled possibility to import ngc file  

  **vdb-config**: fixed bug in file-select-dialog  

  **vdb-config**: wording of public user-repository changed to just user-repository  

  **vdb-dump**: fixed bug in -X ( hex ) mode  

  **vdb-dump, vfs**: addressed obscure bug preventing access to a single external reference  

  **vdb-validate**: fixed handling of empty cells affecting certain databases  





## SRA Toolkit 2.10.1

**December 16, 2019**



  **sra-tools**: changed version to match that of _ncbi-vdb_





## SRA Toolkit 2.10.0

**August 19, 2019**

build/Makefile.env

+2 −2
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@@ -356,8 +356,8 @@ DLLX ?= $(SHLX) 
ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)



# default tool parameters

CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

CFLAGS	= -std=gnu11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

CPFLAGS = -std=gnu++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)

LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)



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

build/Makefile.install

+2 −6
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@@ -69,10 +69,6 @@ installexes: 
	@ echo "Installing executables to $(INST_BINDIR)/..."

	@ mkdir -p $(INST_BINDIR)

	@ $(MAKE) -s --no-print-directory -f $(TOP)/build/Makefile.install $(TOOLS_TO_INSTALL)

	@ # copy the driver 

	 $(COPY) $(TOP)/tools/driver-tool/sratools.pl $(INST_BINDIR)/sratools$(VERSION_EXEX)

	 ln -f -s sratools$(VERSION_EXEX) $(INST_BINDIR)/sratools$(MAJVERS_EXEX)

	 ln -f -s sratools$(MAJVERS_EXEX) $(INST_BINDIR)/sratools$(EXEX)

	@ #

	@ printf "Installing magic file..."

	@ $(COPY) $(TOP)/tools/copycat/magic $(INST_BINDIR) && echo "done"
@@ -132,7 +128,7 @@ endif 
#



TO_UNINSTALL = $(addsuffix *,$(addprefix $(INST_BINDIR)/,$(TOOLS_TO_INSTALL) \

				magic sratools sratools.pl))

				magic ))

ifneq (true, $(LINUX_ROOT))

    TO_UNINSTALL += $(INST_BINDIR)/ncbi/certs.kfg $(INST_BINDIR)/ncbi/ncbi-vdb.kfg $(INST_BINDIR)/ncbi/default.kfg $(INST_BINDIR)/ncbi/vdb-copy.kfg

endif

build/Makefile.shell

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@@ -116,7 +116,7 @@ endif 


# determine SRCDIR

ifdef MODULE

    SRCDIR=$(TOP)/$(MODULE)

    override SRCDIR=$(TOP)/$(MODULE)

else

    SRCDIR=$(TOP)

endif

build/Makefile.tools

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@@ -17,12 +17,12 @@ TOOLS_TO_COPY = \ 
	vdb-config      \

	vdb-copy        \

	vdb-decrypt     \

	vdb-dump        \

	vdb-encrypt     \

	vdb-lock        \

	vdb-passwd      \

	vdb-unlock      \

	vdb-validate    \

	sratools        \



# these tools will be copied to <instdir>/<toolname>-orig;

# <toolname> will be created as a symlink to sratools
@@ -33,6 +33,7 @@ TOOLS_TO_SYMLINK = \ 
	prefetch        \

	srapath         \

	sra-pileup      \

	vdb-dump        \



# these tools may be missing from $(BINDIR), not an error

TOOLS_TO_COPY_OPTIONAL = \