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heathsc / gemBS-rs

A re-write of the gemBS pipeline framework in Rust
BSD 3-Clause "New" or "Revised" License
4 stars 1 forks source link

Installation issues #3

Closed sunabcun closed 3 years ago

sunabcun commented 3 years ago

Hi, I have tried to install gemBS in multiple ways: gemBS, gemBS-rs, container images(like singularity), and Bioconda.

  1. gemBS/gemBS-rs: failing compilation (I have attached parts of words from the errors when I tried gemBS-rs compiling.) , it seems to have a errors.txt errors.txt

    similar issue when it passed around bcf tools even in gemBS.

  2. container image- it works but when I even tried to check the example run from the tutorials gemBS prepare -c example.conf -t example.csv. It says either example.conf does not exist or example.csv does not exist although I have run the code in the folder which has both files.

  3. Bioconda download is consistently failed as well. I tried to install other programs like samtools etc., and all of them worked. I checked if it exists using conda search, and it showed that bioconda channel has gemBS but the connection was frozen and not moving forward.

I'm very frustrated since I can't even compile gemBS or run the tutorial data set (the 1st step: "prepare" part).

heathsc commented 3 years ago

Sorry to hear about your problems with installation and testing. From the error files you provide it looks as though you will need to install libssl and libcom_err to be able to finish compilation.

For the container issues - can you tell me which version of singularity you are using? With earlier versions (2.x I think) it was often the case that only the home filesystem was mounted by default in the container, so if you ran it from a mounted filesystem (I see you were running on gpfs) it is possible that the files were not accessible. In the instructions for the previous version of gemBS (v3) I included instructions for dealing with this issue (see http://statgen.cnag.cat/gemBS/v3/UserGuide/_build/html/containers.html)

sunabcun commented 3 years ago

Thank you for the reply.

I am using school’s HPC and they are not allowed to let me use sudo for installing it. So, I have tried now in my local setting but it still seems to have issues. I have attached the error after installing all required things including libssl and libcom_err. And, I will try it with singularity issue as well.

From: Simon @.> Sent: Thursday, March 25, 2021 4:32 AM To: @.> Cc: Yuna @.>; @.> Subject: Re: [heathsc/gemBS-rs] Installation issues (#3)

Sorry to hear about your problems with installation and testing. From the error files you provide it looks as though you will need to install libssl and libcom_err to be able to finish compilation.

For the container issues - can you tell me which version of singularity you are using? With earlier versions (2.x I think) it was often the case that only the home filesystem was mounted by default in the container, so if you ran it from a mounted filesystem (I see you were running on gpfs) it is possible that the files were not accessible. In the instructions for the previous version of gemBS (v3) I included instructions for dealing with this issue (see http://statgen.cnag.cat/gemBS/v3/UserGuide/_build/html/containers.htmlhttps://urldefense.com/v3/__http:/statgen.cnag.cat/gemBS/v3/UserGuide/_build/html/containers.html__;!!PhOWcWs!g7RSxwFJnrFUjkrm6GxSLVDt46dS5d2WsjUTyaKZpIJlSeuk0GPZ-1Uz4Yx1aMir_TY$)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/heathsc/gemBS-rs/issues/3*issuecomment-806464183__;Iw!!PhOWcWs!g7RSxwFJnrFUjkrm6GxSLVDt46dS5d2WsjUTyaKZpIJlSeuk0GPZ-1Uz4Yx1bS7ajo4$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ALGWH6K7VAEZQBIAG5I4VFTTFLYIDANCNFSM4ZY23U3Q__;!!PhOWcWs!g7RSxwFJnrFUjkrm6GxSLVDt46dS5d2WsjUTyaKZpIJlSeuk0GPZ-1Uz4Yx1qNQcWdc$.

@.*VirtualBox:~/gemBS-rs$ make install make -f Makefile.gemBS install make[1]: Entering directory '/home/yuna/gemBS-rs' make -C c_tools make[2]: Entering directory '/home/yuna/gemBS-rs/c_tools' make --directory=gem3-mapper make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper' make --directory=resources release make[4]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/resources' make[4]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/resources' make --directory=src release make[4]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src' make --directory=align release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align' make --directory=pattern release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align/pattern' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align/pattern' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align' make --directory=approximate_search release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/approximate_search' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/approximate_search' make --directory=archive release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive' make --directory=builder release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/builder' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/builder' make --directory=search release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/search' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/search' make --directory=score release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/score' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/score' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive' make --directory=filtering release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering' make --directory=candidates release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/candidates' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/candidates' make --directory=region release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region' make --directory=region_profile release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region_profile' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region_profile' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering' make --directory=fm_index release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index' make --directory=sa_builder release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/sa_builder' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/sa_builder' make --directory=bwt release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/bwt' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/bwt' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index' make --directory=gpu release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/gpu' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/gpu' make --directory=io release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/io' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/io' make --directory=mapper release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/mapper' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/mapper' make --directory=matches release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches' make --directory=align release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/align' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/align' make --directory=classify release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/classify' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/classify' make --directory=scaffold release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/scaffold' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/scaffold' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches' make --directory=neighborhood_search release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/neighborhood_search' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/neighborhood_search' make --directory=profiler release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/profiler' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/profiler' make --directory=search_pipeline release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/search_pipeline' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/search_pipeline' make --directory=stats release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/stats' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/stats' make --directory=system release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/system' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/system' make --directory=text release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/text' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/text' make --directory=utils release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/utils' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/utils' make --directory=tools release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools' make --directory=interface release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools/interface' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools/interface' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools' make[4]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src' make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper' make --directory=htslib && make --directory=htslib install make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' mkdir -p -m 755 /home/yuna/gemBS-rs/c_tools/tmp_root/bin /home/yuna/gemBS-rs/c_tools/tmp_root/include /home/yuna/gemBS-rs/c_tools/tmp_root/include/htslib /home/yuna/gemBS-rs/c_tools/tmp_root/lib /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man1 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man5 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man7 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p -m 644 libhts.so /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so.1.11 ln -sf libhts.so.1.11 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so ln -sf libhts.so.1.11 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so.3 sed -e *@.@@.@@.PACKAGE_VERSION@#1.11#g' htslib.pc.tmp > /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig/htslib.pc chmod 644 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig/htslib.pc install -p bgzip htsfile tabix /home/yuna/gemBS-rs/c_tools/tmp_root/bin if test -n ""; then install -p ; fi install -p -m 644 htslib/*.h /home/yuna/gemBS-rs/c_tools/tmp_root/include/htslib install -p -m 644 libhts.a /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man7 make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make --directory=htslib -f Makefile.bgzip-shared bgzip-shared && cp htslib/bgzip-shared /home/yuna/gemBS-rs/c_tools/tmp_root/bin/bgzip make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' gcc -fvisibility=hidden -o bgzip-shared bgzip.o -L. -lhts -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make --directory=samtools all make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/samtools' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/samtools' make bin/bcftools make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools' make --directory=bcftools all make[4]: Entering directory '/home/yuna/gemBS-rs/c_tools/bcftools' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/yuna/gemBS-rs/c_tools/bcftools' make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools' make[2]: Leaving directory '/home/yuna/gemBS-rs/c_tools' make -C rust make[2]: Entering directory '/home/yuna/gemBS-rs/rust' GEMBS_INSTALL_ROOT=/usr/local/lib/gemBS RUSTFLAGS="-L /home/yuna/gemBS-rs/c_tools/tmp_root/lib" cargo build --release /bin/sh: 1: cargo: not found make[2]: [Makefile:10: all] Error 127 make[2]: Leaving directory '/home/yuna/gemBS-rs/rust' make[1]: [Makefile.gemBS:60: rust] Error 2 make[1]: Leaving directory '/home/yuna/gemBS-rs' make: *** [Makefile:7: install] Error 2

heathsc commented 3 years ago

It looks like you might not have rust installed in your local setting. Have you tried installing with:

curl https://sh.rustup.rs -sSf > rust.sh && sh rust.sh -y

?

sunabcun commented 3 years ago

Thank you for suggesting. So, I previously installed the rust but I reinstalled again and it works until last moment and it made executable gemBS but it showed these errors: Finished release [optimized] target(s) in 21m 29s cp target/release/gem_bs bin/gemBS cp target/release/read_filter bin/ cp target/release/bs_call bin/ cp target/release/snpxtr bin/ cp target/release/mextr bin/ cp target/release/dbsnp_index bin/ make[2]: Leaving directory '/home/yuna/gemBS-rs/rust'

copy shell script gemBS to a directory in your PATH (i.e., /usr/local/bin or /home/yuna/bin)

echo "#!/bin/sh" > gemBS echo 'LD_LIBRARY_PATH=/usr/local/lib/gemBS/lib:$LD_LIBRARY_PATH /usr/local/lib/gemBS/bin/gemBS $@' >> gemBS chmod 755 gemBS mkdir -p /usr/local/lib/gemBS mkdir: cannot create directory ‘/usr/local/lib/gemBS’: Permission denied make[1]: [Makefile.gemBS:65: /usr/local/lib/gemBS] Error 1 make[1]: Leaving directory '/home/yuna/gemBS-rs' make: [Makefile:7: install] Error 2

So, I tried to execute again with sudo make install. But, it was not working and I did delete whole gemBS_rs folder and re-install all the things again. And, I still get the similar empty container error and it was not resolved by installing rust again. Interestingly, if I execute “make install” not “ sudo make install”, I got the similar error again from the first attempt->

make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' mkdir -p -m 755 /home/yuna/gemBS-rs/c_tools/tmp_root/bin /home/yuna/gemBS-rs/c_tools/tmp_root/include /home/yuna/gemBS-rs/c_tools/tmp_root/include/htslib /home/yuna/gemBS-rs/c_tools/tmp_root/lib /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man1 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man5 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man7 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p -m 644 libhts.so /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so.1.11 install: cannot remove '/home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so.1.11': Permission denied make[3]: [Makefile:562: install-so] Error 1 make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make[2]: [Makefile:43: /home/yuna/gemBS-rs/c_tools/tmp_root/include/htslib/hts.h] Error 2 make[2]: Leaving directory '/home/yuna/gemBS-rs/c_tools' make[1]: [Makefile.gemBS:60: c_tools] Error 2 make[1]: Leaving directory '/home/yuna/gemBS-rs' make: [Makefile:7: install] Error 2

I have attached the result(text files) from “sudo make install” after removing everything as well.

From: Simon @.> Sent: Thursday, March 25, 2021 5:01 AM To: @.> Cc: Yuna @.>; @.> Subject: Re: [heathsc/gemBS-rs] Installation issues (#3)

It looks like you might not have rust installed in your local setting. Have you tried installing with:

curl https://sh.rustup.rshttps://urldefense.com/v3/__https:/sh.rustup.rs__;!!PhOWcWs!h0IpLo0KXddX5-ETV1jDz-2Wycre7LPLtnTX19_bSN01h_mmrSYoaB_6kcBOs976vOM$ -sSf > rust.sh && sh rust.sh -y

?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/heathsc/gemBS-rs/issues/3*issuecomment-806481335__;Iw!!PhOWcWs!h0IpLo0KXddX5-ETV1jDz-2Wycre7LPLtnTX19_bSN01h_mmrSYoaB_6kcBO0H7eIms$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ALGWH6JLO2QEW56HZLX7QGLTFL3XFANCNFSM4ZY23U3Q__;!!PhOWcWs!h0IpLo0KXddX5-ETV1jDz-2Wycre7LPLtnTX19_bSN01h_mmrSYoaB_6kcBObw6R74A$.

make -C rust make[2]: Entering directory '/home/yuna/gemBS-rs/rust' cp gemBS/Cargo.toml.in gemBS/Cargo.toml echo default = [\"slurm\"] >> gemBS/Cargo.toml mkdir bin GEMBS_INSTALL_ROOT=/usr/local/lib/gemBS RUSTFLAGS="-L /home/yuna/gemBS-rs/c_tools/tmp_root/lib" cargo build --release /bin/sh: 1: cargo: not found make[2]: [Makefile:10: all] Error 127 make[2]: Leaving directory '/home/yuna/gemBS-rs/rust' make[1]: [Makefile.gemBS:60: rust] Error 2 make[1]: Leaving directory '/home/yuna/gemBS-rs' make: [Makefile:7: install] Error 2 @.VirtualBox:~/gemBS-rs$ curl https://sh.rustup.rs -sSf > rust.sh && sh rust.sh -y info: downloading installer info: profile set to 'default' info: default host triple is x86_64-unknown-linux-gnu warning: Updating existing toolchain, profile choice will be ignored info: syncing channel updates for 'stable-x86_64-unknown-linux-gnu' info: default toolchain set to 'stable-x86_64-unknown-linux-gnu'

stable-x86_64-unknown-linux-gnu unchanged - rustc 1.50.0 (cb75ad5db 2021-02-10)

Rust is installed now. Great!

To get started you need Cargo's bin directory ($HOME/.cargo/bin) in your PATH environment variable. Next time you log in this will be done automatically.

To configure your current shell, run: source $HOME/.cargo/env @.VirtualBox:~/gemBS-rs$ source $HOME/.cargo/env @.VirtualBox:~/gemBS-rs$ sudo make install make -f Makefile.gemBS install make[1]: Entering directory '/home/yuna/gemBS-rs' make -C c_tools make[2]: Entering directory '/home/yuna/gemBS-rs/c_tools' make --directory=gem3-mapper make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper' make --directory=resources release make[4]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/resources' make[4]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/resources' make --directory=src release make[4]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src' make --directory=align release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align' make --directory=pattern release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align/pattern' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align/pattern' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/align' make --directory=approximate_search release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/approximate_search' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/approximate_search' make --directory=archive release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive' make --directory=builder release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/builder' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/builder' make --directory=search release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/search' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/search' make --directory=score release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/score' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive/score' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/archive' make --directory=filtering release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering' make --directory=candidates release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/candidates' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/candidates' make --directory=region release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region' make --directory=region_profile release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region_profile' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering/region_profile' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/filtering' make --directory=fm_index release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index' make --directory=sa_builder release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/sa_builder' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/sa_builder' make --directory=bwt release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/bwt' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index/bwt' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/fm_index' make --directory=gpu release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/gpu' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/gpu' make --directory=io release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/io' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/io' make --directory=mapper release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/mapper' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/mapper' make --directory=matches release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches' make --directory=align release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/align' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/align' make --directory=classify release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/classify' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/classify' make --directory=scaffold release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/scaffold' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches/scaffold' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/matches' make --directory=neighborhood_search release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/neighborhood_search' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/neighborhood_search' make --directory=profiler release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/profiler' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/profiler' make --directory=search_pipeline release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/search_pipeline' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/search_pipeline' make --directory=stats release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/stats' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/stats' make --directory=system release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/system' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/system' make --directory=text release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/text' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/text' make --directory=utils release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/utils' make[5]: Nothing to be done for 'release'. make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/utils' make --directory=tools release make[5]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools' make --directory=interface release make[6]: Entering directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools/interface' make[6]: Nothing to be done for 'release'. make[6]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools/interface' make[5]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src/tools' make[4]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper/src' make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/gem3-mapper' make --directory=htslib && make --directory=htslib install make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' mkdir -p -m 755 /home/yuna/gemBS-rs/c_tools/tmp_root/bin /home/yuna/gemBS-rs/c_tools/tmp_root/include /home/yuna/gemBS-rs/c_tools/tmp_root/include/htslib /home/yuna/gemBS-rs/c_tools/tmp_root/lib /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man1 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man5 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man7 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p -m 644 libhts.so /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so.1.11 ln -sf libhts.so.1.11 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so ln -sf libhts.so.1.11 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.so.3 sed -e @.@@.@@.PACKAGE_VERSION@#1.11#g' htslib.pc.tmp > /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig/htslib.pc chmod 644 /home/yuna/gemBS-rs/c_tools/tmp_root/lib/pkgconfig/htslib.pc install -p bgzip htsfile tabix /home/yuna/gemBS-rs/c_tools/tmp_root/bin if test -n ""; then install -p ; fi install -p -m 644 htslib/.h /home/yuna/gemBS-rs/c_tools/tmp_root/include/htslib install -p -m 644 libhts.a /home/yuna/gemBS-rs/c_tools/tmp_root/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /home/yuna/gemBS-rs/c_tools/tmp_root/share/man/man7 make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make --directory=htslib -f Makefile.bgzip-shared bgzip-shared && cp htslib/bgzip-shared /home/yuna/gemBS-rs/c_tools/tmp_root/bin/bgzip make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/htslib' gcc -fvisibility=hidden -o bgzip-shared bgzip.o -L. -lhts -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/htslib' make --directory=samtools all make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools/samtools' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools/samtools' make bin/bcftools make[3]: Entering directory '/home/yuna/gemBS-rs/c_tools' make --directory=bcftools all make[4]: Entering directory '/home/yuna/gemBS-rs/c_tools/bcftools' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/yuna/gemBS-rs/c_tools/bcftools' make[3]: Leaving directory '/home/yuna/gemBS-rs/c_tools' make[2]: Leaving directory '/home/yuna/gemBS-rs/c_tools' make -C rust make[2]: Entering directory '/home/yuna/gemBS-rs/rust' GEMBS_INSTALL_ROOT=/usr/local/lib/gemBS RUSTFLAGS="-L /home/yuna/gemBS-rs/c_tools/tmp_root/lib" cargo build --release /bin/sh: 1: cargo: not found make[2]: ** [Makefile:10: all] Error 127 make[2]: Leaving directory '/home/yuna/gemBS-rs/rust' make[1]: [Makefile.gemBS:60: rust] Error 2 make[1]: Leaving directory '/home/yuna/gemBS-rs' make: *** [Makefile:7: install] Error 2

heathsc commented 3 years ago

By default the installation directory is /usr/local/lib/gemBS. You can either run the install using sudo or change the installation directory by editing gemBS_config.mk.in and re-running the install.

Simon

sunabcun commented 3 years ago

Hi Simon, I have tried to install following your suggestion and it works. And, regarding the odd behavior in singularity run, it seems like my HPC-singularity has some issues with calling the program properly. It doesn’t have issues when I ran it in my local computer. I am asking my HPC people to install gemBS since I don’t have a permission but glad to know it doesn’t have an issue to install the program itself. Many thanks and I will close my ticket!

From: Simon @.> Sent: Thursday, March 25, 2021 6:31 AM To: @.> Cc: Yuna @.>; @.> Subject: Re: [heathsc/gemBS-rs] Installation issues (#3)

By default the installation directory is /usr/local/lib/gemBS. You can either run the install using sudo or change the installation directory by editing gemBS_config.mk.in and re-running the install.

Simon

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