<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36525?offset=220 https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome Thu, 08 Aug 2024 23:31:18 -0500 https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome <![CDATA[Tools to access the quality of your assembled genome !]]>
  • FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
  • GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
  • ASSEMBLATHON STATS: Assembly statistics
  • GENOMETOOLS GT STAT: Annotation statistics
  • NCBI FCS ADAPTOR: Adaptor contamination pass/fail
  • NCBI FCS GX: Foreign organism contamination pass/fail
  • BUSCO: Gene-space completeness estimation
  • TIDK: Telomere repeat identification
  • LAI: Continuity of repetitive sequences
  • KRAKEN2: Taxonomy classification
  • HIC CONTACT MAP: Alignment and visualisation of HiC data
  • MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
  • MERQURY: K-mer completeness, consensus quality and phasing assessment
    • ]]>     LEGE     https://bioinformaticsonline.com/blog/view/44754/early-genome-screening-the-new-health-horoscope Thu, 02 Jan 2025 19:44:36 -0600 https://bioinformaticsonline.com/blog/view/44754/early-genome-screening-the-new-health-horoscope <![CDATA[Early Genome Screening: The New Health Horoscope!]]> In an era where precision medicine is reshaping healthcare, genome screening is emerging as the modern equivalent of a health horoscope. It offers insights into our biological "stars," unraveling predispositions to various conditions and empowering individuals with knowledge to navigate their health journeys proactively. But how reliable is this "horoscope," and how does it impact our lives?

    Understanding Genome Screening

    Genome screening involves analyzing an individual's DNA to identify genetic variations that may influence health and disease susceptibility. This can range from simple single-gene tests to comprehensive whole-genome sequencing. By peering into our genetic blueprint, we can uncover risks for conditions like cancer, diabetes, cardiovascular diseases, and even rare genetic disorders.

    The process is straightforward: a saliva or blood sample is collected, and advanced sequencing technologies decipher the genetic code. The results provide a personalized health map, guiding lifestyle modifications, preventive measures, or medical interventions.

    A Shift from Reactive to Proactive Healthcare

    Traditional healthcare often focuses on treating diseases after they manifest. Genome screening flips this model on its head, enabling a shift toward prevention and early intervention. For instance:

    • Cancer Risk Management: Individuals with BRCA1 or BRCA2 gene mutations can opt for enhanced screening programs or preventive surgeries to mitigate their risk of breast and ovarian cancers.

    • Cardiovascular Health: Genetic predispositions to conditions like familial hypercholesterolemia can prompt early cholesterol monitoring and lifestyle adjustments.

    • Rare Diseases: Identifying carriers of genetic disorders can aid in family planning and reduce the incidence of inherited conditions.

    The Ethical and Practical Concerns

    While genome screening offers incredible promise, it is not without challenges:

    1. Accuracy and Interpretation: Genetic predisposition does not guarantee disease. Misinterpretation of results can lead to unnecessary anxiety or unwarranted medical interventions.

    2. Privacy and Data Security: Genetic data is highly sensitive. Ensuring robust data protection measures is crucial to prevent misuse.

    3. Accessibility and Equity: High costs and limited availability may restrict access to genome screening, exacerbating health disparities.

    Balancing Science and Pseudoscience

    The comparison of genome screening to horoscopes isn’t entirely unfounded. Both offer predictive insights, but the scientific foundation of genome screening distinguishes it from astrology. Unlike the alignment of celestial bodies, genetic predictions are based on rigorous data and evidence. However, the probabilistic nature of genetic predispositions underscores the importance of interpreting results in conjunction with clinical and lifestyle factors.

    The Road Ahead

    As genome screening becomes more affordable and integrated into routine healthcare, its potential to transform lives is immense. Policymakers, healthcare providers, and genetic counselors must collaborate to ensure ethical implementation, public awareness, and equitable access.

    Imagine a future where your genetic "horoscope" is a trusted guide, not just a prediction. Early genome screening could help chart a healthier path for generations, making it a cornerstone of personalized medicine. After all, our genes might just hold the key to unlocking a future of better health and well-being.

     

    ]]>     LEGE     https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies Sat, 20 Sep 2025 09:34:04 -0500 https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies <![CDATA[HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies]]> HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.

    panHiTE

    We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

    For detailed instructions, please refer to the panHiTE tutorial.

    Address of the bookmark: https://github.com/CSU-KangHu/HiTE

    ]]>     LEGE     https://bioinformaticsonline.com/pages/view/36185/installing-bioscf-perl-module Mon, 09 Apr 2018 04:04:29 -0500 https://bioinformaticsonline.com/pages/view/36185/installing-bioscf-perl-module <![CDATA[Installing Bio::SCF perl module]]> Most Perl modules are written in Perl, some use XS (they are written in C) so require a C compiler (it's easy to get this setup - don't panic), see your OS of choice below to find out how to get the right compiler. Modules may have dependencies on other modules (almost always on CPAN) and cannot be installed without them (or without a specific version of them). Many modules on CPAN require a somewhat recent version of Perl (version 5.8 or above).

    More about the basic perl module installation steps check this http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

    installing Bio::SCF perl module is daunting task, specieally because of it dependencies. Here is the steps, you need to follow to sucessfully install Bio::SCF module

    #sudo apt-get install libbio-scf-perl #trev for visualization of scf file

    1. You will need the zlib library which can be found at http://www.zlib.net/.

    install zlib library first:

    jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] ./configure []
    Checking for gcc...
    Checking for shared library support...
    Building shared library libz.so.1.2.11 with gcc.
    Checking for size_t... Yes.
    Checking for off64_t... Yes.
    Checking for fseeko... Yes.
    Checking for strerror... Yes.
    Checking for unistd.h... Yes.
    Checking for stdarg.h... Yes.
    Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
    Checking for vsnprintf() in stdio.h... Yes.
    Checking for return value of vsnprintf()... Yes.
    Checking for attribute(visibility) support... Yes.
    jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] make []
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
    ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
    gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
    gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
    rm -f libz.so libz.so.1
    ln -s libz.so.1.2.11 libz.so
    ln -s libz.so.1.2.11 libz.so.1
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.11
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.11
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
    gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
    jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] sudo make install []
    [sudo] password for jitendra:
    rm -f /usr/local/lib/libz.a
    cp libz.a /usr/local/lib
    chmod 644 /usr/local/lib/libz.a
    cp libz.so.1.2.11 /usr/local/lib
    chmod 755 /usr/local/lib/libz.so.1.2.11
    rm -f /usr/local/share/man/man3/zlib.3
    cp zlib.3 /usr/local/share/man/man3
    chmod 644 /usr/local/share/man/man3/zlib.3
    rm -f /usr/local/lib/pkgconfig/zlib.pc
    cp zlib.pc /usr/local/lib/pkgconfig
    chmod 644 /usr/local/lib/pkgconfig/zlib.pc
    rm -f /usr/local/include/zlib.h /usr/local/include/zconf.h
    cp zlib.h zconf.h /usr/local/include
    chmod 644 /usr/local/include/zlib.h /usr/local/include/zconf.h
     


    2. Now make io_lib-1.9

    In order to install this perl extension you have to install io-lib version 1.9 or higher from the Staden library (staden.sourceforge.net). This can be downloaded from https://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243&release_id=340318 confirm that the package installed correctly look for a library named "libread".

    jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] export CFLAGS="-fPIC" && ./configure
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for gawk... gawk
    checking whether make sets $(MAKE)... yes
    checking for gcc... gcc
    checking for C compiler default output file name... a.out
    checking whether the C compiler works... yes
    checking whether we are cross compiling... no
    checking for suffix of executables...
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ANSI C... none needed
    checking for style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking for a BSD-compatible install... /usr/bin/install -c
    checking for ranlib... ranlib
    checking for main in -lz... yes
    checking how to run the C preprocessor... gcc -E
    checking for egrep... grep -E
    checking for ANSI C header files... yes
    checking for sys/wait.h that is POSIX.1 compatible... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking fcntl.h usability... yes
    checking fcntl.h presence... yes
    checking for fcntl.h... yes
    checking limits.h usability... yes
    checking limits.h presence... yes
    checking for limits.h... yes
    checking for unistd.h... (cached) yes
    checking zlib.h usability... yes
    checking zlib.h presence... yes
    checking for zlib.h... yes
    checking whether byte ordering is bigendian... no
    checking for short... yes
    checking size of short... 2
    checking for int... yes
    checking size of int... 4
    checking for long... yes
    checking size of long... 8
    checking for inline... inline
    checking for mode_t... yes
    checking build system type... x86_64-unknown-linux-gnu
    checking host system type... x86_64-unknown-linux-gnu
    checking for cos in -lm... yes
    checking for strdup... yes
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating read/Makefile
    config.status: creating progs/Makefile
    config.status: creating config.h
    config.status: executing depfiles commands
    jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] make []
    make all-recursive
    make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
    Making all in read
    make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT Read.o -MD -MP -MF ".deps/Read.Tpo" -c -o Read.o Read.c; \
    then mv -f ".deps/Read.Tpo" ".deps/Read.Po"; else rm -f ".deps/Read.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_extras.o -MD -MP -MF ".deps/scf_extras.Tpo" -c -o scf_extras.o scf_extras.c; \
    then mv -f ".deps/scf_extras.Tpo" ".deps/scf_extras.Po"; else rm -f ".deps/scf_extras.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT translate.o -MD -MP -MF ".deps/translate.Tpo" -c -o translate.o translate.c; \
    then mv -f ".deps/translate.Tpo" ".deps/translate.Po"; else rm -f ".deps/translate.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compression.o -MD -MP -MF ".deps/compression.Tpo" -c -o compression.o `test -f '../ztr/compression.c' || echo './'`../ztr/compression.c; \
    then mv -f ".deps/compression.Tpo" ".deps/compression.Po"; else rm -f ".deps/compression.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr.o -MD -MP -MF ".deps/ztr.Tpo" -c -o ztr.o `test -f '../ztr/ztr.c' || echo './'`../ztr/ztr.c; \
    then mv -f ".deps/ztr.Tpo" ".deps/ztr.Po"; else rm -f ".deps/ztr.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr_translate.o -MD -MP -MF ".deps/ztr_translate.Tpo" -c -o ztr_translate.o `test -f '../ztr/ztr_translate.c' || echo './'`../ztr/ztr_translate.c; \
    then mv -f ".deps/ztr_translate.Tpo" ".deps/ztr_translate.Po"; else rm -f ".deps/ztr_translate.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT fpoint.o -MD -MP -MF ".deps/fpoint.Tpo" -c -o fpoint.o `test -f '../abi/fpoint.c' || echo './'`../abi/fpoint.c; \
    then mv -f ".deps/fpoint.Tpo" ".deps/fpoint.Po"; else rm -f ".deps/fpoint.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOABI.o -MD -MP -MF ".deps/seqIOABI.Tpo" -c -o seqIOABI.o `test -f '../abi/seqIOABI.c' || echo './'`../abi/seqIOABI.c; \
    then mv -f ".deps/seqIOABI.Tpo" ".deps/seqIOABI.Po"; else rm -f ".deps/seqIOABI.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOALF.o -MD -MP -MF ".deps/seqIOALF.Tpo" -c -o seqIOALF.o `test -f '../alf/seqIOALF.c' || echo './'`../alf/seqIOALF.c; \
    then mv -f ".deps/seqIOALF.Tpo" ".deps/seqIOALF.Po"; else rm -f ".deps/seqIOALF.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ctfCompress.o -MD -MP -MF ".deps/ctfCompress.Tpo" -c -o ctfCompress.o `test -f '../ctf/ctfCompress.c' || echo './'`../ctf/ctfCompress.c; \
    then mv -f ".deps/ctfCompress.Tpo" ".deps/ctfCompress.Po"; else rm -f ".deps/ctfCompress.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOCTF.o -MD -MP -MF ".deps/seqIOCTF.Tpo" -c -o seqIOCTF.o `test -f '../ctf/seqIOCTF.c' || echo './'`../ctf/seqIOCTF.c; \
    then mv -f ".deps/seqIOCTF.Tpo" ".deps/seqIOCTF.Po"; else rm -f ".deps/seqIOCTF.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT expFileIO.o -MD -MP -MF ".deps/expFileIO.Tpo" -c -o expFileIO.o `test -f '../exp_file/expFileIO.c' || echo './'`../exp_file/expFileIO.c; \
    then mv -f ".deps/expFileIO.Tpo" ".deps/expFileIO.Po"; else rm -f ".deps/expFileIO.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOPlain.o -MD -MP -MF ".deps/seqIOPlain.Tpo" -c -o seqIOPlain.o `test -f '../plain/seqIOPlain.c' || echo './'`../plain/seqIOPlain.c; \
    then mv -f ".deps/seqIOPlain.Tpo" ".deps/seqIOPlain.Po"; else rm -f ".deps/seqIOPlain.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT misc_scf.o -MD -MP -MF ".deps/misc_scf.Tpo" -c -o misc_scf.o `test -f '../scf/misc_scf.c' || echo './'`../scf/misc_scf.c; \
    then mv -f ".deps/misc_scf.Tpo" ".deps/misc_scf.Po"; else rm -f ".deps/misc_scf.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_scf.o -MD -MP -MF ".deps/read_scf.Tpo" -c -o read_scf.o `test -f '../scf/read_scf.c' || echo './'`../scf/read_scf.c; \
    then mv -f ".deps/read_scf.Tpo" ".deps/read_scf.Po"; else rm -f ".deps/read_scf.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT write_scf.o -MD -MP -MF ".deps/write_scf.Tpo" -c -o write_scf.o `test -f '../scf/write_scf.c' || echo './'`../scf/write_scf.c; \
    then mv -f ".deps/write_scf.Tpo" ".deps/write_scf.Po"; else rm -f ".deps/write_scf.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT array.o -MD -MP -MF ".deps/array.Tpo" -c -o array.o `test -f '../utils/array.c' || echo './'`../utils/array.c; \
    then mv -f ".deps/array.Tpo" ".deps/array.Po"; else rm -f ".deps/array.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compress.o -MD -MP -MF ".deps/compress.Tpo" -c -o compress.o `test -f '../utils/compress.c' || echo './'`../utils/compress.c; \
    then mv -f ".deps/compress.Tpo" ".deps/compress.Po"; else rm -f ".deps/compress.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT error.o -MD -MP -MF ".deps/error.Tpo" -c -o error.o `test -f '../utils/error.c' || echo './'`../utils/error.c; \
    then mv -f ".deps/error.Tpo" ".deps/error.Po"; else rm -f ".deps/error.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT files.o -MD -MP -MF ".deps/files.Tpo" -c -o files.o `test -f '../utils/files.c' || echo './'`../utils/files.c; \
    then mv -f ".deps/files.Tpo" ".deps/files.Po"; else rm -f ".deps/files.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT find.o -MD -MP -MF ".deps/find.Tpo" -c -o find.o `test -f '../utils/find.c' || echo './'`../utils/find.c; \
    then mv -f ".deps/find.Tpo" ".deps/find.Po"; else rm -f ".deps/find.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mach-io.o -MD -MP -MF ".deps/mach-io.Tpo" -c -o mach-io.o `test -f '../utils/mach-io.c' || echo './'`../utils/mach-io.c; \
    then mv -f ".deps/mach-io.Tpo" ".deps/mach-io.Po"; else rm -f ".deps/mach-io.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT open_trace_file.o -MD -MP -MF ".deps/open_trace_file.Tpo" -c -o open_trace_file.o `test -f '../utils/open_trace_file.c' || echo './'`../utils/open_trace_file.c; \
    then mv -f ".deps/open_trace_file.Tpo" ".deps/open_trace_file.Po"; else rm -f ".deps/open_trace_file.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_alloc.o -MD -MP -MF ".deps/read_alloc.Tpo" -c -o read_alloc.o `test -f '../utils/read_alloc.c' || echo './'`../utils/read_alloc.c; \
    then mv -f ".deps/read_alloc.Tpo" ".deps/read_alloc.Po"; else rm -f ".deps/read_alloc.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT strings.o -MD -MP -MF ".deps/strings.Tpo" -c -o strings.o `test -f '../utils/strings.c' || echo './'`../utils/strings.c; \
    then mv -f ".deps/strings.Tpo" ".deps/strings.Po"; else rm -f ".deps/strings.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT traceType.o -MD -MP -MF ".deps/traceType.Tpo" -c -o traceType.o `test -f '../utils/traceType.c' || echo './'`../utils/traceType.c; \
    then mv -f ".deps/traceType.Tpo" ".deps/traceType.Po"; else rm -f ".deps/traceType.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT xalloc.o -MD -MP -MF ".deps/xalloc.Tpo" -c -o xalloc.o `test -f '../utils/xalloc.c' || echo './'`../utils/xalloc.c; \
    then mv -f ".deps/xalloc.Tpo" ".deps/xalloc.Po"; else rm -f ".deps/xalloc.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT vlen.o -MD -MP -MF ".deps/vlen.Tpo" -c -o vlen.o `test -f '../utils/vlen.c' || echo './'`../utils/vlen.c; \
    then mv -f ".deps/vlen.Tpo" ".deps/vlen.Po"; else rm -f ".deps/vlen.Tpo"; exit 1; fi
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_table.o -MD -MP -MF ".deps/hash_table.Tpo" -c -o hash_table.o `test -f '../utils/hash_table.c' || echo './'`../utils/hash_table.c; \
    then mv -f ".deps/hash_table.Tpo" ".deps/hash_table.Po"; else rm -f ".deps/hash_table.Tpo"; exit 1; fi
    ../utils/hash_table.c: In function ‘HashFileOpen’:
    ../utils/hash_table.c:920:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
    sprintf(aname, "%.*s%s", cp-fname+1, fname, hf->archive);
    ^
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mFILE.o -MD -MP -MF ".deps/mFILE.Tpo" -c -o mFILE.o `test -f '../utils/mFILE.c' || echo './'`../utils/mFILE.c; \
    then mv -f ".deps/mFILE.Tpo" ".deps/mFILE.Po"; else rm -f ".deps/mFILE.Tpo"; exit 1; fi
    rm -f libread.a
    ar cru libread.a Read.o scf_extras.o translate.o compression.o ztr.o ztr_translate.o fpoint.o seqIOABI.o seqIOALF.o ctfCompress.o seqIOCTF.o expFileIO.o seqIOPlain.o misc_scf.o read_scf.o write_scf.o array.o compress.o error.o files.o find.o mach-io.o open_trace_file.o read_alloc.o strings.o traceType.o xalloc.o vlen.o hash_table.o mFILE.o
    ar: `u' modifier ignored since `D' is the default (see `U')
    ranlib libread.a
    make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
    Making all in progs
    make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT convert_trace.o -MD -MP -MF ".deps/convert_trace.Tpo" -c -o convert_trace.o convert_trace.c; \
    then mv -f ".deps/convert_trace.Tpo" ".deps/convert_trace.Po"; else rm -f ".deps/convert_trace.Tpo"; exit 1; fi
    gcc -fPIC -o convert_trace convert_trace.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT makeSCF.o -MD -MP -MF ".deps/makeSCF.Tpo" -c -o makeSCF.o makeSCF.c; \
    then mv -f ".deps/makeSCF.Tpo" ".deps/makeSCF.Po"; else rm -f ".deps/makeSCF.Tpo"; exit 1; fi
    gcc -fPIC -o makeSCF makeSCF.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT extract_seq.o -MD -MP -MF ".deps/extract_seq.Tpo" -c -o extract_seq.o extract_seq.c; \
    then mv -f ".deps/extract_seq.Tpo" ".deps/extract_seq.Po"; else rm -f ".deps/extract_seq.Tpo"; exit 1; fi
    gcc -fPIC -o extract_seq extract_seq.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT index_tar.o -MD -MP -MF ".deps/index_tar.Tpo" -c -o index_tar.o index_tar.c; \
    then mv -f ".deps/index_tar.Tpo" ".deps/index_tar.Po"; else rm -f ".deps/index_tar.Tpo"; exit 1; fi
    gcc -fPIC -o index_tar index_tar.o
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_dump.o -MD -MP -MF ".deps/scf_dump.Tpo" -c -o scf_dump.o scf_dump.c; \
    then mv -f ".deps/scf_dump.Tpo" ".deps/scf_dump.Po"; else rm -f ".deps/scf_dump.Tpo"; exit 1; fi
    gcc -fPIC -o scf_dump scf_dump.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_info.o -MD -MP -MF ".deps/scf_info.Tpo" -c -o scf_info.o scf_info.c; \
    then mv -f ".deps/scf_info.Tpo" ".deps/scf_info.Po"; else rm -f ".deps/scf_info.Tpo"; exit 1; fi
    gcc -fPIC -o scf_info scf_info.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_update.o -MD -MP -MF ".deps/scf_update.Tpo" -c -o scf_update.o scf_update.c; \
    then mv -f ".deps/scf_update.Tpo" ".deps/scf_update.Po"; else rm -f ".deps/scf_update.Tpo"; exit 1; fi
    gcc -fPIC -o scf_update scf_update.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT get_comment.o -MD -MP -MF ".deps/get_comment.Tpo" -c -o get_comment.o get_comment.c; \
    then mv -f ".deps/get_comment.Tpo" ".deps/get_comment.Po"; else rm -f ".deps/get_comment.Tpo"; exit 1; fi
    gcc -fPIC -o get_comment get_comment.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_tar.o -MD -MP -MF ".deps/hash_tar.Tpo" -c -o hash_tar.o hash_tar.c; \
    then mv -f ".deps/hash_tar.Tpo" ".deps/hash_tar.Po"; else rm -f ".deps/hash_tar.Tpo"; exit 1; fi
    gcc -fPIC -o hash_tar hash_tar.o ../read/libread.a -lz -lm
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_extract.o -MD -MP -MF ".deps/hash_extract.Tpo" -c -o hash_extract.o hash_extract.c; \
    then mv -f ".deps/hash_extract.Tpo" ".deps/hash_extract.Po"; else rm -f ".deps/hash_extract.Tpo"; exit 1; fi
    gcc -fPIC -o hash_extract hash_extract.o ../read/libread.a -lz -lm
    if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT trace_dump.o -MD -MP -MF ".deps/trace_dump.Tpo" -c -o trace_dump.o trace_dump.c; \
    then mv -f ".deps/trace_dump.Tpo" ".deps/trace_dump.Po"; else rm -f ".deps/trace_dump.Tpo"; exit 1; fi
    gcc -fPIC -o trace_dump trace_dump.o ../read/libread.a -lz -lm
    ../read/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
    make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
    make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
    make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

    jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] sudo make install []
    [sudo] password for jitendra:
    Making install in read
    make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
    make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
    test -z "/usr/local/lib" || mkdir -p -- "/usr/local/lib"
    /usr/bin/install -c -m 644 'libread.a' '/usr/local/lib/libread.a'
    ranlib '/usr/local/lib/libread.a'
    make[2]: Nothing to be done for 'install-data-am'.
    make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
    make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
    Making install in progs
    make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
    make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
    test -z "/usr/local/bin" || mkdir -p -- "/usr/local/bin"
    /usr/bin/install -c 'convert_trace' '/usr/local/bin/convert_trace'
    /usr/bin/install -c 'makeSCF' '/usr/local/bin/makeSCF'
    /usr/bin/install -c 'extract_seq' '/usr/local/bin/extract_seq'
    /usr/bin/install -c 'index_tar' '/usr/local/bin/index_tar'
    /usr/bin/install -c 'scf_dump' '/usr/local/bin/scf_dump'
    /usr/bin/install -c 'scf_info' '/usr/local/bin/scf_info'
    /usr/bin/install -c 'scf_update' '/usr/local/bin/scf_update'
    /usr/bin/install -c 'get_comment' '/usr/local/bin/get_comment'
    /usr/bin/install -c 'hash_tar' '/usr/local/bin/hash_tar'
    /usr/bin/install -c 'hash_extract' '/usr/local/bin/hash_extract'
    /usr/bin/install -c 'trace_dump' '/usr/local/bin/trace_dump'
    make[2]: Nothing to be done for 'install-data-am'.
    make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
    make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
    make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
    make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
    make[2]: Nothing to be done for 'install-exec-am'.
    test -z "/usr/local/man/man3" || mkdir -p -- "/usr/local/man/man3"
    /usr/bin/install -c -m 644 './man/man3/exp2read.3' '/usr/local/man/man3/exp2read.3'
    /usr/bin/install -c -m 644 './man/man3/ExperimentFile.3' '/usr/local/man/man3/ExperimentFile.3'
    /usr/bin/install -c -m 644 './man/man3/fread_reading.3' '/usr/local/man/man3/fread_reading.3'
    /usr/bin/install -c -m 644 './man/man3/fread_scf.3' '/usr/local/man/man3/fread_scf.3'
    /usr/bin/install -c -m 644 './man/man3/fwrite_reading.3' '/usr/local/man/man3/fwrite_reading.3'
    /usr/bin/install -c -m 644 './man/man3/fwrite_scf.3' '/usr/local/man/man3/fwrite_scf.3'
    /usr/bin/install -c -m 644 './man/man3/read2exp.3' '/usr/local/man/man3/read2exp.3'
    /usr/bin/install -c -m 644 './man/man3/read2scf.3' '/usr/local/man/man3/read2scf.3'
    /usr/bin/install -c -m 644 './man/man3/read_allocate.3' '/usr/local/man/man3/read_allocate.3'
    /usr/bin/install -c -m 644 './man/man3/read_deallocate.3' '/usr/local/man/man3/read_deallocate.3'
    /usr/bin/install -c -m 644 './man/man3/read_reading.3' '/usr/local/man/man3/read_reading.3'
    /usr/bin/install -c -m 644 './man/man3/read_scf.3' '/usr/local/man/man3/read_scf.3'
    /usr/bin/install -c -m 644 './man/man3/read_scf_header.3' '/usr/local/man/man3/read_scf_header.3'
    /usr/bin/install -c -m 644 './man/man3/scf2read.3' '/usr/local/man/man3/scf2read.3'
    /usr/bin/install -c -m 644 './man/man3/write_reading.3' '/usr/local/man/man3/write_reading.3'
    /usr/bin/install -c -m 644 './man/man3/write_scf.3' '/usr/local/man/man3/write_scf.3'
    /usr/bin/install -c -m 644 './man/man3/write_scf_header.3' '/usr/local/man/man3/write_scf_header.3'
    test -z "/usr/local/man/man4" || mkdir -p -- "/usr/local/man/man4"
    /usr/bin/install -c -m 644 './man/man4/Read.4' '/usr/local/man/man4/Read.4'
    test -z "/usr/local/include/io_lib" || mkdir -p -- "/usr/local/include/io_lib"
    /usr/bin/install -c -m 644 'read/Read.h' '/usr/local/include/io_lib/Read.h'
    /usr/bin/install -c -m 644 'read/scf_extras.h' '/usr/local/include/io_lib/scf_extras.h'
    /usr/bin/install -c -m 644 'read/translate.h' '/usr/local/include/io_lib/translate.h'
    /usr/bin/install -c -m 644 'abi/abi.h' '/usr/local/include/io_lib/abi.h'
    /usr/bin/install -c -m 644 'abi/fpoint.h' '/usr/local/include/io_lib/fpoint.h'
    /usr/bin/install -c -m 644 'abi/seqIOABI.h' '/usr/local/include/io_lib/seqIOABI.h'
    /usr/bin/install -c -m 644 'alf/alf.h' '/usr/local/include/io_lib/alf.h'
    /usr/bin/install -c -m 644 'ctf/seqIOCTF.h' '/usr/local/include/io_lib/seqIOCTF.h'
    /usr/bin/install -c -m 644 'exp_file/expFileIO.h' '/usr/local/include/io_lib/expFileIO.h'
    /usr/bin/install -c -m 644 'plain/plain.h' '/usr/local/include/io_lib/plain.h'
    /usr/bin/install -c -m 644 'scf/scf.h' '/usr/local/include/io_lib/scf.h'
    /usr/bin/install -c -m 644 'utils/array.h' '/usr/local/include/io_lib/array.h'
    /usr/bin/install -c -m 644 'utils/compress.h' '/usr/local/include/io_lib/compress.h'
    /usr/bin/install -c -m 644 'utils/error.h' '/usr/local/include/io_lib/error.h'
    /usr/bin/install -c -m 644 'utils/mach-io.h' '/usr/local/include/io_lib/mach-io.h'
    /usr/bin/install -c -m 644 'utils/misc.h' '/usr/local/include/io_lib/misc.h'
    /usr/bin/install -c -m 644 'utils/open_trace_file.h' '/usr/local/include/io_lib/open_trace_file.h'
    /usr/bin/install -c -m 644 'utils/tar_format.h' '/usr/local/include/io_lib/tar_format.h'
    /usr/bin/install -c -m 644 'utils/traceType.h' '/usr/local/include/io_lib/traceType.h'
    /usr/bin/install -c -m 644 'utils/xalloc.h' '/usr/local/include/io_lib/xalloc.h'
    /usr/bin/install -c -m 644 'utils/mFILE.h' '/usr/local/include/io_lib/mFILE.h'
    /usr/bin/install -c -m 644 'utils/stdio_hack.h' '/usr/local/include/io_lib/stdio_hack.h'
    /usr/bin/install -c -m 644 'utils/vlen.h' '/usr/local/include/io_lib/vlen.h'
    /usr/bin/install -c -m 644 'utils/hash_table.h' '/usr/local/include/io_lib/hash_table.h'
    /usr/bin/install -c -m 644 'utils/os.h' '/usr/local/include/io_lib/os.h'
    /usr/bin/install -c -m 644 'ztr/compression.h' '/usr/local/include/io_lib/compression.h'
    /usr/bin/install -c -m 644 'ztr/ztr.h' '/usr/local/include/io_lib/ztr.h'
    make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
    make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

    3. Now install Bio::SCF

    Now follows these steps:

    tar zxf Bio::SCF.tar
    cd Bio::SCF
    perl Makefile.PL
    make
    make test
    make install

    jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] perl Makefile.PL []
    Checking if your kit is complete...
    Looks good
    Generating a Unix-style Makefile
    Writing Makefile for Bio::SCF
    Writing MYMETA.yml and MYMETA.json
    jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] make []
    cp SCF.pm blib/lib/Bio/SCF.pm
    cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm
    Running Mkbootstrap for Bio::SCF ()
    chmod 644 "SCF.bs"
    "/usr/bin/perl" "/usr/share/perl/5.22/ExtUtils/xsubpp" -typemap "/usr/share/perl/5.22/ExtUtils/typemap" SCF.xs > SCF.xsc && mv SCF.xsc SCF.c
    Please specify prototyping behavior for SCF.xs (see perlxs manual)
    x86_64-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE" -DLITTLE_ENDIAN SCF.c
    In file included from /usr/lib/x86_64-linux-gnu/perl/5.22/CORE/perl.h:5546:0,
    from SCF.xs:5:
    SCF.xs: In function ‘XS_Bio__SCF_get_scf_pointer’:
    SCF.xs:57:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
    ret_val = newSViv((int)scf_data);
    ^
    /usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
    #define newSViv(a) Perl_newSViv(aTHX_ a)
    ^
    SCF.xs: In function ‘XS_Bio__SCF_get_scf_fpointer’:
    SCF.xs:80:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
    ret_val = newSViv((int)scf_data);
    ^
    /usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
    #define newSViv(a) Perl_newSViv(aTHX_ a)
    ^
    SCF.xs: In function ‘XS_Bio__SCF_scf_free’:
    SCF.xs:89:17: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    scf_deallocate((Scf *)scf_pointer);
    ^
    SCF.xs: In function ‘XS_Bio__SCF_get_comments’:
    SCF.xs:95:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_set_comments’:
    SCF.xs:108:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_scf_write’:
    SCF.xs:121:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_scf_fwrite’:
    SCF.xs:137:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_get_from_header’:
    SCF.xs:159:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_get_at’:
    SCF.xs:186:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_set_base_at’:
    SCF.xs:242:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    SCF.xs: In function ‘XS_Bio__SCF_set_at’:
    SCF.xs:255:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    Scf *scf_data = (Scf *)scf_pointer;
    ^
    rm -f blib/arch/auto/Bio/SCF/SCF.so
    x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \
    -lread -lz \

    /usr/local/lib/libread.a(open_trace_file.o): In function `find_file_url':
    open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
    chmod 755 blib/arch/auto/Bio/SCF/SCF.so
    "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644
    Manifying 1 pod document

    ]]>     Jit     https://bioinformaticsonline.com/fun/view/39329/you-cant-install-david-brownlee Wed, 01 May 2019 21:47:36 -0500 https://bioinformaticsonline.com/fun/view/39329/you-cant-install-david-brownlee <![CDATA[You can't install David Brownlee ;-)]]> By mistake I ask cpan to install abs, and it return this message.

    jitendra@jitendra-Aspire-S3-391[parallelLastz] sudo cpan install abs  [ 4:43AM]
    Going to read '/home/jitendra/.cpan/Metadata'
      Database was generated on Thu, 02 May 2019 00:08:06 GMT
    Don't be silly, you can't install David Brownlee ;-)

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics Sat, 31 May 2014 15:41:16 -0500 https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics <![CDATA[Linux Sort Commands for Bioinformatics]]> Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.

    sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
    sort input.txt

    sort a huge file (GNU sort ONLY):
    sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

    sort starting from the third column, skipping the first two columns:
    sort +2 input.txt

    sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
    sort -k2,2nr -k3,3 input.txt

    sort starting from the 4th character at column 2, as numbers:
    sort -k2.4n input.txt

    More Linxu sort command information

    If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

    man sort

    or

    sort --help

    on your Unix/Linux system.

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/pages/view/27965/cheatsheet-for-linux Wed, 22 Jun 2016 07:55:06 -0500 https://bioinformaticsonline.com/pages/view/27965/cheatsheet-for-linux <![CDATA[Cheatsheet for Linux !!]]> Linux Commands Cheat Sheet

        File System

        ls — list items in current directory

        ls -l — list items in current directory and show in long format to see perimissions, size, an modification date

        ls -a — list all items in current directory, including hidden files

        ls -F — list all items in current directory and show directories with a slash and executables with a star

        ls dir — list all items in directory dir

        cd dir — change directory to dir

        cd .. — go up one directory

        cd / — go to the root directory

        cd ~ — go to to your home directory

        cd - — go to the last directory you were just in

        pwd — show present working directory

        mkdir dir — make directory dir

        rm file — remove file

        rm -r dir — remove directory dir recursively

        cp file1 file2 — copy file1 to file2

        cp -r dir1 dir2 — copy directory dir1 to dir2 recursively

        mv file1 file2 — move (rename) file1 to file2

        ln -s file link — create symbolic link to file

        touch file — create or update file

        cat file — output the contents of file

        less file — view file with page navigation

        head file — output the first 10 lines of file

        tail file — output the last 10 lines of file

        tail -f file — output the contents of file as it grows, starting with the last 10 lines

        vim file — edit file

        alias name 'command' — create an alias for a command
        System

        shutdown — shut down machine

        reboot — restart machine

        date — show the current date and time

        whoami — who you are logged in as

        finger user — display information about user

        man command — show the manual for command

        df — show disk usage

        du — show directory space usage

        free — show memory and swap usage

        whereis app — show possible locations of app

        which app — show which app will be run by default
        Process Management

        ps — display your currently active processes

        top — display all running processes

        kill pid — kill process id pid

        kill -9 pid — force kill process id pid
        Permissions

        ls -l — list items in current directory and show permissions

        chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.

        7 — full permissions

        6 — read and write only

        5 — read and execute only

        4 — read only

        3 — write and execute only

        2 — write only

        1 — execute only

        0 — no permissions

        chmod 600 file — you can read and write - good for files

        chmod 700 file — you can read, write, and execute - good for scripts

        chmod 644 file — you can read and write, and everyone else can only read - good for web pages

        chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
        Networking

        wget file — download a file

        curl file — download a file

        scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine

        scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server

        scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine

        ssh user@host — connect to host as user

        ssh -p port user@host — connect to host on port as user

        ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login

        ping host — ping host and output results

        whois domain — get information for domain

        dig domain — get DNS information for domain

        dig -x host — reverse lookup host

        lsof -i tcp:1337 — list all processes running on port 1337
        Searching

        grep pattern files — search for pattern in files

        grep -r pattern dir — search recursively for pattern in dir

        grep -rn pattern dir — search recursively for pattern in dir and show the line number found

        grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension

        command | grep pattern — search for pattern in the output of command

        find file — find all instances of file in real system

        locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find

        sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
        Compression

        tar cf file.tar files — create a tar named file.tar containing files

        tar xf file.tar — extract the files from file.tar

        tar czf file.tar.gz files — create a tar with Gzip compression

        tar xzf file.tar.gz — extract a tar using Gzip

        gzip file — compresses file and renames it to file.gz

        gzip -d file.gz — decompresses file.gz back to file
        Shortcuts

        ctrl+a — move cursor to beginning of line

        ctrl+f — move cursor to end of line

        alt+f — move cursor forward 1 word

        alt+b — move cursor backward 1 word

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf Sun, 16 Feb 2020 02:57:40 -0600 <![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]> https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html
    Your profile:
    Degree in bioinformatics, biostatistics, or equivalent
    Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing
    Strong competence in working in Unix/Linux environments (shell)
    Strong programming skills (in particular: Python, R, Perl)
    Experience with using git and snakemake
    Fluent English language skills, both spoken and written
    Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team

    Additional Information:

    If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

    Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

    Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

    Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.

    ]]>         https://bioinformaticsonline.com/bookmarks/view/43120/ventoy-an-open-source-tool-to-create-bootable-usb-drive Tue, 29 Jun 2021 10:16:19 -0500 https://bioinformaticsonline.com/bookmarks/view/43120/ventoy-an-open-source-tool-to-create-bootable-usb-drive <![CDATA[Ventoy: an open source tool to create bootable USB drive]]> Ventoy is an open source tool to create bootable USB drive for ISO/WIM/IMG/VHD(x)/EFI files. With ventoy, you don't need to format the disk over and over, you just need to copy the image files to the USB drive and boot it. You can copy many image files at a time and ventoy will give you a boot menu to select them. x86 Legacy BIOS, IA32 UEFI, x86_64 UEFI, ARM64 UEFI and MIPS64EL UEFI are supported in the same way. Both MBR and GPT partition style are supported in the same way. Most type of OS supported(Windows/WinPE/Linux/Unix/Vmware/Xen...) 700+ ISO files are tested. 

    Address of the bookmark: https://github.com/ventoy/Ventoy

    ]]>     LEGE     https://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools Tue, 16 Jul 2013 14:30:30 -0500 https://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools <![CDATA[List of popular bioinformatics software/tools]]> In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.

    Address of the bookmark: http://samtools.sourceforge.net/swlist.shtml

    ]]>     Jitendra Narayan