error during installation: failed with error code 1 in /tmp/pip-install-pvy5rtw7/quicksect/

Alice Mayer

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Mar 22, 2019, 12:27:32 PM3/22/19

to majiq_voila

Hello,

I’m sorry to bother you. I’m trying to install Majiq and have an error message.

I’ve used the command

> pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

I’ve installed it in a new conda environment that has python, pysam and numpy

About dependencies, I have the following versions:

Python 3.7.2

pip 19.0.3 from /home/u/u230707/miniconda3/envs/majiq/lib/python3.7/site-packages/pip (python 3.7)

git version 1.8.3.1

gcc (GCC) 5.1.0

zlib:            1.2.11-h14c3975_1004       conda-forge

Cython version 0.29.6

pysam-0.15.2

numpy-1.16.2 

The problem seems to come from the gcc command. I’ve copied below the whole process and error message. The end of it says:

Command "/home/u/u230707/miniconda3/envs/majiq/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-pvy5rtw7/quicksect/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-rmtelyag/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-pvy5rtw7/quicksect/

Looking at a recent post on the google forum, I’ve seen that it could be a problem of configuration of miniconda and gcc/ld. Therefore, I’ve tried to change the name of miniconda ld as advised in the post, using

(majiq) u23...@genetic.master01 ~ $ mv /home/u/u230707/miniconda3/envs/majiq/compiler_compat/ld /home/u/u230707/miniconda3/envs/majiq/compiler_compat/ld-conda

I’ve then run the installation again and it didn’t work. The error message is the same (except the name of the temporary pip-install-folder)

Could you help me throubleshoot?

Thank you very much,

Best wishes,

Alice

The output of `pip freeze` is the following:

certifi==2019.3.9

Cython==0.29.6

h5py==2.9.0

numpy==1.16.2

pysam==0.15.2

scipy==1.2.1

six==1.11.0

Standard out of the pip install:

(majiq) u23...@genetic.master01 ~ $ pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

Collecting majiq from git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

  Cloning https://bitbucket.org/biociphers/majiq_stable.git to /tmp/pip-install-pvy5rtw7/majiq

Requirement already satisfied: Cython>=0.27.3 in ./miniconda3/envs/majiq/lib/python3.7/site-packages (from majiq) (0.29.6)

Requirement already satisfied: pysam>=0.14 in ./miniconda3/envs/majiq/lib/python3.7/site-packages (from majiq) (0.15.2)

Requirement already satisfied: numpy>=1.14.1 in ./miniconda3/envs/majiq/lib/python3.7/site-packages (from majiq) (1.16.2)

Collecting scipy>=1.1.0 (from majiq)

  Downloading https://files.pythonhosted.org/packages/3e/7e/5cee36eee5b3194687232f6150a89a38f784883c612db7f4da2ab190980d/scipy-1.2.1-cp37-cp37m-manylinux1_x86_64.whl (24.8MB)

    100% |████████████████████████████████| 24.8MB 349kB/s 

Collecting h5py>=2.7.1 (from majiq)

  Downloading https://files.pythonhosted.org/packages/8e/fd/2ca5c4f4ed33ac4178f9c4d551e3946ab480866e3cd67a65a67a4bb35367/h5py-2.9.0-cp37-cp37m-manylinux1_x86_64.whl (2.8MB)

    100% |████████████████████████████████| 2.8MB 2.8MB/s 

Collecting quicksect>=0.2.0 (from majiq)

  Downloading https://files.pythonhosted.org/packages/88/a6/d1e8fadda67eb10d633d32b2b4d6232e853d51aa1f793605afbfcd684377/quicksect-0.2.0.tar.gz (65kB)

    100% |████████████████████████████████| 71kB 7.8MB/s 

Collecting matplotlib>=2.1.2 (from majiq)

  Downloading https://files.pythonhosted.org/packages/83/2a/e47bbd9396af32376863a426baed62d9bf3091f81defd1fe81c5f33b11a3/matplotlib-3.0.3-cp37-cp37m-manylinux1_x86_64.whl (13.0MB)

    100% |████████████████████████████████| 13.0MB 732kB/s 

Collecting cycler==0.10.0 (from majiq)

  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl

Collecting Jinja2==2.10 (from majiq)

  Downloading https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl (126kB)

    100% |████████████████████████████████| 133kB 9.2MB/s 

Collecting MarkupSafe==1.0 (from majiq)

  Downloading https://files.pythonhosted.org/packages/4d/de/32d741db316d8fdb7680822dd37001ef7a448255de9699ab4bfcbdf4172b/MarkupSafe-1.0.tar.gz

Collecting psutil==5.4.3 (from majiq)

  Downloading https://files.pythonhosted.org/packages/e2/e1/600326635f97fee89bf8426fef14c5c29f4849c79f68fd79f433d8c1bd96/psutil-5.4.3.tar.gz (412kB)

    100% |████████████████████████████████| 419kB 8.4MB/s 

Collecting pyparsing==2.2.0 (from majiq)

  Downloading https://files.pythonhosted.org/packages/6a/8a/718fd7d3458f9fab8e67186b00abdd345b639976bc7fb3ae722e1b026a50/pyparsing-2.2.0-py2.py3-none-any.whl (56kB)

    100% |████████████████████████████████| 61kB 7.1MB/s 

Collecting python-dateutil==2.6.1 (from majiq)

  Downloading https://files.pythonhosted.org/packages/4b/0d/7ed381ab4fe80b8ebf34411d14f253e1cf3e56e2820ffa1d8844b23859a2/python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)

    100% |████████████████████████████████| 194kB 9.2MB/s 

Collecting pytz==2018.3 (from majiq)

  Downloading https://files.pythonhosted.org/packages/3c/80/32e98784a8647880dedf1f6bf8e2c91b195fe18fdecc6767dcf5104598d6/pytz-2018.3-py2.py3-none-any.whl (509kB)

    100% |████████████████████████████████| 512kB 7.0MB/s 

Collecting six==1.11.0 (from majiq)

  Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl

Collecting SQLAlchemy==1.2.4 (from majiq)

  Downloading https://files.pythonhosted.org/packages/f3/b7/d8725042f105cc6b71c7bae0ffd46e49f762e5a08f421f1eddd855a1f723/SQLAlchemy-1.2.4.tar.gz (5.6MB)

    100% |████████████████████████████████| 5.6MB 1.7MB/s 

Collecting kiwisolver>=1.0.1 (from matplotlib>=2.1.2->majiq)

  Downloading https://files.pythonhosted.org/packages/5c/7e/d6cae2f241ba474a2665f24b480bf4e247036d63939dda2bbc4d2ee5069d/kiwisolver-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (89kB)

    100% |████████████████████████████████| 92kB 8.1MB/s 

Requirement already satisfied: setuptools in ./miniconda3/envs/majiq/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=2.1.2->majiq) (40.8.0)

Building wheels for collected packages: majiq, quicksect, MarkupSafe, psutil, SQLAlchemy

  Building wheel for majiq (setup.py) ... done

  Stored in directory: /tmp/pip-ephem-wheel-cache-jnygfbjv/wheels/00/3d/76/940444754a408b8ff1833f6b3b5986d046f3d20992e2c6ca63

  Building wheel for quicksect (setup.py) ... error

  Complete output from command /home/u/u230707/miniconda3/envs/majiq/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-pvy5rtw7/quicksect/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-pk9766xu --python-tag cp37:

  running bdist_wheel

  running build

  running build_ext

  skipping 'src/quicksect.c' Cython extension (up-to-date)

  building 'quicksect' extension

  creating build

  creating build/temp.linux-x86_64-3.7

  creating build/temp.linux-x86_64-3.7/src

  gcc -pthread -B /home/u/u230707/miniconda3/envs/majiq/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/u/u230707/miniconda3/envs/majiq/include/python3.7m -c src/quicksect.c -o build/temp.linux-x86_64-3.7/src/quicksect.o

  src/quicksect.c: In function ‘__Pyx_PyCFunction_FastCall’:

  src/quicksect.c:9016:12: error: too many arguments to function ‘(PyObject * (*)(PyObject *, PyObject * const*, Py_ssize_t))meth’

       return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);

^

  src/quicksect.c: In function ‘__Pyx__ExceptionSave’:

  src/quicksect.c:9402:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       *type = tstate->exc_type;

^

  src/quicksect.c:9403:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       *value = tstate->exc_value;

^

  src/quicksect.c:9404:17: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       *tb = tstate->exc_traceback;

^

  src/quicksect.c: In function ‘__Pyx__ExceptionReset’:

  src/quicksect.c:9411:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       tmp_type = tstate->exc_type;

^

  src/quicksect.c:9412:23: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       tmp_value = tstate->exc_value;

^

  src/quicksect.c:9413:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       tmp_tb = tstate->exc_traceback;

^

  src/quicksect.c:9414:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       tstate->exc_type = type;

^

  src/quicksect.c:9415:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       tstate->exc_value = value;

^

  src/quicksect.c:9416:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       tstate->exc_traceback = tb;

^

  src/quicksect.c: In function ‘__Pyx__GetException’:

  src/quicksect.c:9471:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       tmp_type = tstate->exc_type;

^

  src/quicksect.c:9472:23: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       tmp_value = tstate->exc_value;

^

  src/quicksect.c:9473:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       tmp_tb = tstate->exc_traceback;

^

  src/quicksect.c:9474:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       tstate->exc_type = local_type;

^

  src/quicksect.c:9475:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       tstate->exc_value = local_value;

^

  src/quicksect.c:9476:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       tstate->exc_traceback = local_tb;

^

  src/quicksect.c: In function ‘__Pyx__ExceptionSwap’:

  src/quicksect.c:10574:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       tmp_type = tstate->exc_type;

^

  src/quicksect.c:10575:23: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       tmp_value = tstate->exc_value;

^

  src/quicksect.c:10576:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       tmp_tb = tstate->exc_traceback;

^

  src/quicksect.c:10577:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

       tstate->exc_type = *type;

^

  src/quicksect.c:10578:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

       tstate->exc_value = *value;

^

  src/quicksect.c:10579:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

       tstate->exc_traceback = *tb;

^

  error: command 'gcc' failed with exit status 1

  ----------------------------------------

  Failed building wheel for quicksect

  Running setup.py clean for quicksect

  Building wheel for MarkupSafe (setup.py) ... done

  Stored in directory: /home/u/u230707/.cache/pip/wheels/33/56/20/ebe49a5c612fffe1c5a632146b16596f9e64676768661e4e46

  Building wheel for psutil (setup.py) ... done

  Stored in directory: /home/u/u230707/.cache/pip/wheels/fe/33/84/baea3d665de2d1af7e8f827f3883811bba5e4149443ccf8191

  Building wheel for SQLAlchemy (setup.py) ... done

  Stored in directory: /home/u/u230707/.cache/pip/wheels/bc/0a/6a/9d6a6f3ee714fd2e910a3299786c6ce54599f46dbda4b0b2cd

Successfully built majiq MarkupSafe psutil SQLAlchemy

Failed to build quicksect

Installing collected packages: scipy, six, h5py, quicksect, pyparsing, python-dateutil, kiwisolver, cycler, matplotlib, MarkupSafe, Jinja2, psutil, pytz, SQLAlchemy, majiq

  Running setup.py install for quicksect ... error

    Complete output from command /home/u/u230707/miniconda3/envs/majiq/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-pvy5rtw7/quicksect/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-rmtelyag/install-record.txt --single-version-externally-managed --compile:

    running install

    running build

    running build_ext

    skipping 'src/quicksect.c' Cython extension (up-to-date)

    building 'quicksect' extension

    creating build

    creating build/temp.linux-x86_64-3.7

    creating build/temp.linux-x86_64-3.7/src

    gcc -pthread -B /home/u/u230707/miniconda3/envs/majiq/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/u/u230707/miniconda3/envs/majiq/include/python3.7m -c src/quicksect.c -o build/temp.linux-x86_64-3.7/src/quicksect.o

    src/quicksect.c: In function ‘__Pyx_PyCFunction_FastCall’:

    src/quicksect.c:9016:12: error: too many arguments to function ‘(PyObject * (*)(PyObject *, PyObject * const*, Py_ssize_t))meth’

         return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);

^

    src/quicksect.c: In function ‘__Pyx__ExceptionSave’:

    src/quicksect.c:9402:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         *type = tstate->exc_type;

^

    src/quicksect.c:9403:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         *value = tstate->exc_value;

^

    src/quicksect.c:9404:17: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         *tb = tstate->exc_traceback;

^

    src/quicksect.c: In function ‘__Pyx__ExceptionReset’:

    src/quicksect.c:9411:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         tmp_type = tstate->exc_type;

^

    src/quicksect.c:9412:23: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         tmp_value = tstate->exc_value;

^

    src/quicksect.c:9413:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         tmp_tb = tstate->exc_traceback;

^

    src/quicksect.c:9414:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         tstate->exc_type = type;

^

    src/quicksect.c:9415:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         tstate->exc_value = value;

^

    src/quicksect.c:9416:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         tstate->exc_traceback = tb;

^

    src/quicksect.c: In function ‘__Pyx__GetException’:

    src/quicksect.c:9471:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         tmp_type = tstate->exc_type;

^

    src/quicksect.c:9472:23: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         tmp_value = tstate->exc_value;

^

    src/quicksect.c:9473:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         tmp_tb = tstate->exc_traceback;

^

    src/quicksect.c:9474:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         tstate->exc_type = local_type;

^

    src/quicksect.c:9475:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         tstate->exc_value = local_value;

^

    src/quicksect.c:9476:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         tstate->exc_traceback = local_tb;

^

    src/quicksect.c: In function ‘__Pyx__ExceptionSwap’:

    src/quicksect.c:10574:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         tmp_type = tstate->exc_type;

^

    src/quicksect.c:10575:23: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         tmp_value = tstate->exc_value;

^

    src/quicksect.c:10576:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         tmp_tb = tstate->exc_traceback;

^

    src/quicksect.c:10577:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’

         tstate->exc_type = *type;

^

    src/quicksect.c:10578:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’

         tstate->exc_value = *value;

^

    src/quicksect.c:10579:11: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’

         tstate->exc_traceback = *tb;

^

    error: command 'gcc' failed with exit status 1

    ----------------------------------------

Command "/home/u/u230707/miniconda3/envs/majiq/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-pvy5rtw7/quicksect/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-rmtelyag/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-pvy5rtw7/quicksect/

Kiran Paul

unread,

Mar 22, 2019, 12:35:53 PM3/22/19

to Alice Mayer, majiq_voila

Hello Alice,

I too had a similar issue when I was trying to install it in my Anaconda environment. Then I tried installing it outside the my Conda environment and it worked. Some the dependencies seems to have an issue with the Conda environment.

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Regards
Kiran V Paul
Bioinformatics Analyst-PRA
Medical Oncology
Anschutz Medical Campus

Jose luis

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Mar 24, 2019, 10:08:06 AM3/24/19

to majiq_voila

I searched a bit on the internet and didn't find anything directly related to this but just a hint that maybe this problem is related to quickset and python 3.7. Try a fresh environment using python 3.6, you can specify python=3.6, that is what im using (it should install python 3.6.8).

José Luis

cmuc...@gmail.com

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Apr 3, 2019, 11:14:29 AM4/3/19

to majiq_voila

Hello,

Would there be a solution other than getting out of Anaconda? I'm a bit lost in BASH without that environment.

Thanks

Christian

Jordi Vaquero

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Apr 3, 2019, 5:07:49 PM4/3/19

to majiq_voila

Hello,

Do you know if this error has been triggered with majiq2?

Thanks

Jordi

cmuc...@gmail.com

unread,

Apr 5, 2019, 4:04:10 AM4/5/19

to majiq_voila

Hi Jordi,

Sorry I don't understand your question.

Christian

Le vendredi 22 mars 2019 17:27:32 UTC+1, Alice Mayer a écrit :

cmuc...@gmail.com

unread,

Apr 5, 2019, 4:06:55 AM4/5/19

to majiq_voila

Yes. This is about installing the new majiq2.

Christian

Le vendredi 22 mars 2019 17:27:32 UTC+1, Alice Mayer a écrit :

Thiago Britto-Borges

unread,

Apr 5, 2019, 4:32:29 AM4/5/19

to majiq_voila

Hi,

I had experienced the same problems.

My solutions was the following:

Use the following majiq_env.yml to install with conda env create -f majiq_env.yml .

name:

majiq

channels:
- bioconda

dependencies:
- python = 3.5
- GitPython
- wheel
- setuptools
- numpy
- cython
- htslib
- pysam

Next you activate this new env (with conda activate majiq )

Then you can export HTSLIB_INCLUDE_DIR and HTSLIB_LIBRARY_DIR env variables. they should be respectively (conda path)/envs/majiq/lib/python3.5/site-packages/pysam/include/htslib and (conda path)/envs/majiq/lib/python3.5/site-packages/pysam/include/htslib/htslib/ . To get the precise path for htslib you can run ` import pytsam; pysam.get_include() ` within you python enviroment. If the majiq devs add this to the setup.py, the conda installation would work flawlessly.

Finally, you can install majiq with pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq . I found other problems running the tool and I will report thoses as soon I have time.

Alice Mayer

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Apr 5, 2019, 11:47:09 AM4/5/19

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Hi Thiago,

Thank you very much!!!! It was the exports of HTSLIB_INCLUDE_DIR and HTSLIB_LIBRARY_DIR that solved the problem.

I first tried a new conda with python 3.6 as suggested by Jose Luis but it didn't work, then before to try to make again new environment with your yml file, I just exported the 2 environment variables you described and tried the installation again and it worked.

I don't know how you found out what to do from the error message (I'm quite new to bioinfo).

One of the error message was about htslib: `./majiq/src/internals/io_bam.hpp:8:24: fatal error: htslib/sam.h: No such file or directory`

but others were about cc1plus, gcc or wheel...

I still have lots to learn!

Thank you so much!

Alice

Alice Mayer

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Apr 5, 2019, 11:53:01 AM4/5/19

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Thanks Paul,

I didn't want to install out of any conda environment because I didn't want to take the risk of changing something that would affect other programmes...

At the end, Thiago's solutions worked for me.

Here is the whole installation process I used:

```

conda create --name MAJIQ python=3.6 pysam numpy cython
conda activate MAJIQ
export HTSLIB_INCLUDE_DIR=/home/u/u230707/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/pysam/include/htslib/
export HTSLIB_LIBRARY_DIR=/home/u/u230707/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/pysam/include/htslib/htslib/

pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

```

I used python 3.6 as suggested by Jose Luis... But it may also have worked with python3.7

All the best,

Alice

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cmuc...@gmail.com

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Apr 9, 2019, 1:00:11 PM4/9/19

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Hello,

I finally solved my problem.

I'm working on a Mac, and apparently on Macs, Conda fails to install pysam on anything higher than Python 2.7.

Yet, there is a version of pysam that can be installed on Macs and that is compatible with Python3.

I installed it with PIP in my conda environment:

pip install of pysam==0.15.2

and the installation of majiq2 went to completion.

Christian

Jordi Vaquero

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Apr 9, 2019, 1:01:24 PM4/9/19

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Hello,

Pysam is no longer a requirement for majiq 2. We will check to make sure is not in the requirements or instructions.

Thanks

Jordi

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cmuc...@gmail.com

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Apr 9, 2019, 1:53:50 PM4/9/19

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Hi again.

You were right. Pysam wasn't the real problem. I just repeated the installation on my lab computer and got back the old problem.

Any ideas?

Christian

Le vendredi 22 mars 2019 17:27:32 UTC+1, Alice Mayer a écrit :

Jordi Vaquero

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Apr 9, 2019, 2:10:33 PM4/9/19

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One question, are you trying to update majiq over an old installation? MAJIQ 2 doesn’t use quicksect anymore.

Did you tried to delete an recreate the conda environment?

Thanks

From: "majiq...@googlegroups.com" <majiq...@googlegroups.com> on behalf of "cmuc...@gmail.com" <cmuc...@gmail.com>

Date: Tuesday, April 9, 2019 at 1:53 PM
To: majiq_voila <majiq...@googlegroups.com>

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cmuc...@gmail.com

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Apr 9, 2019, 2:22:30 PM4/9/19

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Yes, I'm working in a fresh conda environment.

Christian

Le vendredi 22 mars 2019 17:27:32 UTC+1, Alice Mayer a écrit :

Jack Humphrey

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Apr 19, 2019, 5:53:32 PM4/19/19

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Hi all,

I followed Alice's conda recipe and MAJIQ installs successfully on a linux cluster.

I'm using htslib1.9 and have GNU gcc v 6.2

Majiq installed using the git+ command without any warnings or errors.

However when I run MAJIQ build, it parses the provided GFF3 (gencode human v30) but then the program sits at the "Reading file" stage for the first BAM file.

The BAM files are all toy examples for one known gene with a clear splicing change, only a few 1000 reads.

Running top on the node shows that the majiq process isn't using any CPU or memory.

Is there anyway of being able to diagnose what's gone wrong with the installation?

Jordi Vaquero

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Apr 19, 2019, 9:34:27 PM4/19/19

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Hello Jack,

How did you installed htslib?

Jordi

From: "majiq...@googlegroups.com" <majiq...@googlegroups.com> on behalf of Jack Humphrey <countja...@gmail.com>

Date: Friday, April 19, 2019 at 5:53 PM
To: majiq_voila <majiq...@googlegroups.com>

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Jack Humphrey

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Apr 22, 2019, 1:52:56 PM4/22/19

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Hi Jordi,

I'm using a shared version of htslib installed my hpc maintainers. Would you suggest installing my own local version?

On Friday, 19 April 2019 21:34:27 UTC-4, Jordi Vaquero wrote:

Hello Jack,

How did you installed htslib?

Jordi

From: "majiq...@googlegroups.com" <majiq...@googlegroups.com> on behalf of Jack Humphrey <countja...@gmail.com>
Date: Friday, April 19, 2019 at 5:53 PM
To: majiq_voila <majiq...@googlegroups.com>
Subject: [Majiq] Re: error during installation: failed with error code 1 in /tmp/pip-install-pvy5rtw7/quicksect/

Hi all,

I followed Alice's conda recipe and MAJIQ installs successfully on a linux cluster.

I'm using htslib1.9 and have GNU gcc v 6.2

Majiq installed using the git+ command without any warnings or errors.

However when I run MAJIQ build, it parses the provided GFF3 (gencode human v30) but then the program sits at the "Reading file" stage for the first BAM file.

The BAM files are all toy examples for one known gene with a clear splicing change, only a few 1000 reads.

Running top on the node shows that the majiq process isn't using any CPU or memory.

Is there anyway of being able to diagnose what's gone wrong with the installation?

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Jack Humphrey

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Apr 22, 2019, 1:56:07 PM4/22/19

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I should add I tried setting the HTSLIB_INCLUDE_DIR and HTSLIB_LIBRARY_DIR variables to both the conda pysam paths and to this other path and both had the same problem - succesful installation but then hanging around at the build stage.

I'll try installing my own htslib and try again.

Is there any way to switch on some kind of verbose mode for the build section? I used the --debug flag but it didn't output anything more as build was running.

Jordi Vaquero

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Apr 22, 2019, 6:28:43 PM4/22/19

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I just saw that problem before and it was related with how the htslib was compiled and installed. If you can try installing one we can see if that was the problem.

jordi

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Yaoi T

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Apr 30, 2019, 4:33:15 AM4/30/19

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Hi, Alice and other anaconda users !

According to the following, I installed majiq2.0 successfully as an anaconda3 environment.

OS is Ubuntu 18.04 LTS

I use Anaconda3 of which channels are 'defaults', 'conda-forge' and 'bioconda'.

MAJIQ installation requires GNU GCC>=7.2. I first checked the version of gcc in OS.

$ gcc --version

gcc (Ubuntu 7.3.0-27ubuntu1~18.04) 7.3.0

Because this version is >=7.2, I omitted the installation step of gcc.

Next, I created the conda environment.

$ conda create -n majiq-voila2.0 python=3

Here, the followings besides python-3.7.3 are also installed without using pip command as in the instruction.

pip conda-forge/linux-64::pip-19.1-py37_0

setuptools conda-forge/linux-64::setuptools-41.0.1-py37_0

wheel conda-forge/linux-64::wheel-0.33.1-py37_0

After the activation of the conda environment, you will find that gcc in the OS is also used in in this environment.

(majiq-voila2.0) ~$ gcc --version

gcc (Ubuntu 7.3.0-27ubuntu1~18.04) 7.3.0

Then, I installed another pre-requirements - htslib

(majiq-voila2.0) ~$ conda install -n majiq-voila2.0 htslib

It is important that

" MAJIQ installation assumes the library and its header files are present in the Unix default locations (/usr/local/lib, /usr/local/include). If that is not the case the appropriate locations can be specified setting the following environment variables. "

So, you must input the follows:

$ export HTSLIB_LIBRARY_DIR=/path/to/htslib/lib

$ export HTSLIB_INCLUDE_DIR=/path/to/htslib/include

Here, htslib was installed in environment location(As you know, you can get this location by using the command; conda info -e.):

(majiq-voila2.0) ~$ ls -lh /path/to/anaconda3/envs/majiq-voila2.0

You will find a couple of directory; "include" and "lib"

So I typed as the follows:

(majiq-voila2.0) ~$ export HTSLIB_LIBRARY_DIR=/path/to/anaconda3/envs/majiq-voila2.0/lib

(majiq-voila2.0) ~$ export HTSLIB_INCLUDE_DIR=/path/to/anaconda3/envs/majiq-voila2.0/include

Finally, I install the remaining :

(majiq-voila2.0) ~$ conda install -n majiq-voila2.0 cython numpy gitpython

The environment was reboot, just in case.

(majiq-voila2.0) ~$ conda deactivate

~$ conda activate majiq-voila2.0

Final step is the installation of majiq2.0 by using pip command.

(majiq-voila2.0) ~$ pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

You will find a message in the final line:

Successfully installed Flask-1.0.2 Flask-WTF-0.14.2 Jinja2-2.10.1 MarkupSafe-1.1.1 WTForms-2.2.1 Werkzeug-0.15.2 click-7.0 h5py-2.9.0 itsdangerous-1.1.0 majiq-2.0 psutil-5.6.2 scipy-1.2.1 six-1.12.0 waitress-1.1.0

You also find that the following majiq commands work successfully.

$ majiq -v

$ majiq -h

$ majiq build -h

$ majiq psi -h

$ majiq deltapsi -h

2019年3月23日土曜日 1時27分32秒 UTC+9 Alice Mayer:

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